From b55797a7b9c4952d603a2e94b7f1793c1f925e13 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?B=C3=A9r=C3=A9nice=20Batut?= Date: Mon, 29 Jan 2018 18:07:24 +0100 Subject: [PATCH] Add workflow for paired-end and collection data --- config/workflows/shotgun_workflow_pe.ga | 1 + config/workflows/shotgun_workflow_pe_collection.ga | 1 + config/workflows/shotgun_workflow_se_collection.ga | 1 + 3 files changed, 3 insertions(+) create mode 100644 config/workflows/shotgun_workflow_pe.ga create mode 100644 config/workflows/shotgun_workflow_pe_collection.ga create mode 100644 config/workflows/shotgun_workflow_se_collection.ga diff --git a/config/workflows/shotgun_workflow_pe.ga b/config/workflows/shotgun_workflow_pe.ga new file mode 100644 index 0000000..d6c78a5 --- /dev/null +++ b/config/workflows/shotgun_workflow_pe.ga @@ -0,0 +1 @@ +{"uuid": "cb815700-ad19-4de3-8fb9-23ed99f4a22f", "tags": [], "format-version": "0.1", "name": "Shotgun workflow for paired-end data", "steps": {"0": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{}", "id": 0, "uuid": "da4d90df-bfaf-43be-bb68-82b102d7d492", "errors": null, "name": "Input dataset", "label": "R1 reads", "inputs": [], "position": {"top": 165.5, "left": 143.5}, "annotation": "", "content_id": null, "type": "data_input"}, "1": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{}", "id": 1, "uuid": "b9a10a93-0e4c-443c-82d4-6d1df1885464", "errors": null, "name": "Input dataset", "label": "R2 reads", "inputs": [], "position": {"top": 286.5, "left": 143.5}, "annotation": "", "content_id": null, "type": "data_input"}, "2": {"tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/fastq_join/fastq_join/1.1.2-806.1", "tool_version": "1.1.2-806.1", "outputs": [{"type": "fastqsanger", "name": "outputJoined"}, {"type": "fastqsanger", "name": "outputUnmatched1"}, {"type": "fastqsanger", "name": "outputUnmatched2"}, {"type": "tabular", "name": "outputStitchLengthReport"}], "workflow_outputs": [], "input_connections": {"input_type|read2": {"output_name": "output", "id": 1}, "input_type|read1": {"output_name": "output", "id": 0}}, "tool_state": "{\"__page__\": null, \"stitchLengthReport\": \"\\\"false\\\"\", \"input_type\": \"{\\\"read1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"read2\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"input_type_selector\\\": \\\"paired\\\"}\", \"__rerun_remap_job_id__\": null, \"splitChar\": \"\\\" \\\"\", \"minOverlap\": \"\\\"6\\\"\", \"pctMaxDiff\": \"\\\"8.0\\\"\"}", "id": 2, "tool_shed_repository": {"owner": "lparsons", "changeset_revision": "8ec3dfde378b", "name": "fastq_join", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "a8a601f3-3836-4865-9ec3-03c3f29007d0", "errors": null, "name": "fastq-join", "post_job_actions": {}, "label": null, "inputs": [{"name": "input_type", "description": "runtime parameter for tool fastq-join"}, {"name": "input_type", "description": "runtime parameter for tool fastq-join"}], "position": {"top": 199.5, "left": 386.5}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/fastq_join/fastq_join/1.1.2-806.1", "type": "tool"}, "3": {"tool_id": "c385e49b9fe1853c", "inputs": [], "outputs": [], "subworkflow": {"uuid": "a07c681b-a9c1-472e-bd7a-e5e4bdd736be", "tags": "", "format-version": "0.1", "name": "Shotgun workflow", "steps": {"0": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{}", "id": 0, "uuid": "443cdeb2-5918-423f-8821-1bf732dc678c", "errors": null, "name": "Input dataset", "label": "Raw reads", "inputs": [], "position": {"top": 689, "left": 207}, "annotation": "", "content_id": null, "type": "data_input"}, "1": {"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71", "tool_version": "0.71", "outputs": [{"type": "html", "name": "html_file"}, {"type": "txt", "name": "text_file"}], "workflow_outputs": [], "input_connections": {"input_file": {"output_name": "output", "id": 0}}, "tool_state": "{\"__page__\": null, \"contaminants\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"limits\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "id": 1, "tool_shed_repository": {"owner": "devteam", "changeset_revision": "ff9530579d1f", "name": "fastqc", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "f9aa307f-2e7c-4ebd-948d-011ffcfd5f26", "errors": null, "name": "FastQC", "post_job_actions": {}, "label": "Quality control", "inputs": [{"name": "contaminants", "description": "runtime parameter for tool FastQC"}, {"name": "limits", "description": "runtime parameter for tool FastQC"}, {"name": "input_file", "description": "runtime parameter for tool FastQC"}], "position": {"top": 609, "left": 404}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71", "type": "tool"}, "2": {"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1", "tool_version": "0.4.3.1", "outputs": [{"type": "input", "name": "trimmed_reads_paired_collection"}, {"type": "input", "name": "trimmed_reads_unpaired_collection"}, {"type": "input", "name": "trimmed_reads_single"}, {"type": "input", "name": "trimmed_reads_pair1"}, {"type": "input", "name": "trimmed_reads_pair2"}, {"type": "input", "name": "unpaired_reads_1"}, {"type": "input", "name": "unpaired_reads_2"}, {"type": "txt", "name": "report_file"}], "workflow_outputs": [], "input_connections": {"singlePaired|input_singles": {"output_name": "output", "id": 0}}, "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"params\": \"{\\\"settingsType\\\": \\\"default\\\", \\\"__current_case__\\\": 0}\", \"rrbs\": \"{\\\"settingsType\\\": \\\"default\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"three_prime_clip_R1\\\": \\\"\\\", \\\"trimming\\\": {\\\"trimming_select\\\": \\\"\\\", \\\"__current_case__\\\": 0}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0, \\\"input_singles\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\"}", "id": 2, "tool_shed_repository": {"owner": "bgruening", "changeset_revision": "949f01671246", "name": "trim_galore", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "0533b5d9-7a59-438c-a74b-0b7687f481ea", "errors": null, "name": "Trim Galore!", "post_job_actions": {}, "label": "Trimming", "inputs": [{"name": "singlePaired", "description": "runtime parameter for tool Trim Galore!"}], "position": {"top": 831, "left": 411}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1", "type": "tool"}, "3": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_dereplication/1.9.7.0", "tool_version": "1.9.7.0", "outputs": [{"type": "fasta", "name": "outfile"}, {"type": "fasta", "name": "uc_outfile"}], "workflow_outputs": [], "input_connections": {"infile": {"output_name": "trimmed_reads_single", "id": 2}}, "tool_state": "{\"sizein\": \"\\\"false\\\"\", \"__page__\": null, \"maxuniquesize\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"minuniquesize\": \"\\\"\\\"\", \"topn\": \"\\\"\\\"\", \"strand\": \"\\\"plus\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"sizeout\": \"\\\"false\\\"\", \"uc\": \"\\\"false\\\"\"}", "id": 3, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "576963db5f1b", "name": "vsearch", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "98dc5416-f149-4e69-874c-48c4a8a67b09", "errors": null, "name": "VSearch dereplication", "post_job_actions": {}, "label": "Dereplication", "inputs": [{"name": "infile", "description": "runtime parameter for tool VSearch dereplication"}], "position": {"top": 913, "left": 706}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_dereplication/1.9.7.0", "type": "tool"}, "4": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2/metaphlan2/2.6.0.0", "tool_version": "2.6.0.0", "outputs": [{"type": "tabular", "name": "output_file"}, {"type": "sam", "name": "sam_output_file"}, {"type": "biom", "name": "biom_output_file"}], "workflow_outputs": [], "input_connections": {"input_file": {"output_name": "outfile", "id": 3}}, "tool_state": "{\"min_cu_len\": \"\\\"2000\\\"\", \"min_alignment_len\": \"\\\"0\\\"\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null, \"ignore_eukaryotes\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"db\": \"{\\\"db_selector\\\": \\\"cached\\\", \\\"cached_db\\\": \\\"mpa_v20_m200\\\", \\\"__current_case__\\\": 0}\", \"stat_q\": \"\\\"0.1\\\"\", \"ignore_viruses\": \"\\\"true\\\"\", \"ignore_archaea\": \"\\\"true\\\"\", \"analysis_type\": \"{\\\"tax_lev\\\": \\\"a\\\", \\\"analysis_type_select\\\": \\\"rel_ab\\\", \\\"__current_case__\\\": 0}\", \"ignore_bacteria\": \"\\\"true\\\"\"}", "id": 4, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "8c82c4d90cc6", "name": "metaphlan2", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "7281de8c-c5df-48dd-841a-80c468b5fe75", "errors": null, "name": "MetaPhlAn2", "post_job_actions": {}, "label": "Taxonomic assignation", "inputs": [{"name": "input_file", "description": "runtime parameter for tool MetaPhlAn2"}], "position": {"top": 698, "left": 982}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2/metaphlan2/2.6.0.0", "type": "tool"}, "5": {"tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.5", "tool_version": "2.1b.5", "outputs": [{"type": "input", "name": "output_fastx"}, {"type": "fastq", "name": "output_paired_fastx"}, {"type": "fastq", "name": "aligned_forward"}, {"type": "fastq", "name": "aligned_reverse"}, {"type": "input", "name": "output_other"}, {"type": "fastq", "name": "output_paired_other"}, {"type": "fastq", "name": "unaligned_forward"}, {"type": "fastq", "name": "unaligned_reverse"}, {"type": "bam", "name": "output_bam"}, {"type": "tabular", "name": "output_blast"}, {"type": "txt", "name": "output_biom"}, {"type": "input", "name": "output_de_novo"}, {"type": "txt", "name": "output_log"}], "workflow_outputs": [], "input_connections": {"sequencing_type|reads": {"output_name": "outfile", "id": 3}}, "tool_state": "{\"__page__\": null, \"strand_search\": \"\\\"\\\"\", \"aligned_sam\": \"{\\\"aligned_sam_selector\\\": \\\"--sam\\\", \\\"sq\\\": \\\"false\\\", \\\"__current_case__\\\": 0}\", \"log\": \"\\\"false\\\"\", \"input_reads\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"mismatch\": \"\\\"-3\\\"\", \"sequencing_type\": \"{\\\"reads\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sequencing_type_selector\\\": \\\"not_paired\\\", \\\"__current_case__\\\": 0}\", \"ambiguous_letter\": \"\\\"-3\\\"\", \"aligned_blast\": \"{\\\"__current_case__\\\": 1, \\\"aligned_blast_selector\\\": \\\"\\\"}\", \"databases_type\": \"{\\\"databases_selector\\\": \\\"cached\\\", \\\"input_databases\\\": [\\\"2.1b-silva-bac-23s-id98\\\", \\\"2.1b-silva-bac-16s-id90\\\", \\\"2.1b-silva-euk-28s-id98\\\", \\\"2.1b-rfam-5.8s-database-id98\\\", \\\"2.1b-silva-euk-18s-id95\\\", \\\"2.1b-silva-arc-16s-id95\\\", \\\"2.1b-silva-arc-23s-id98\\\", \\\"2.1b-rfam-5s-database-id98\\\"], \\\"__current_case__\\\": 0}\", \"match\": \"\\\"2\\\"\", \"gap_open\": \"\\\"5\\\"\", \"report\": \"{\\\"report_best\\\": {\\\"report_best_min_lis\\\": \\\"2\\\", \\\"__current_case__\\\": 0, \\\"report_best_type\\\": \\\"1\\\"}, \\\"report_type\\\": \\\"best\\\", \\\"__current_case__\\\": 1, \\\"blast\\\": {\\\"blast_output\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"print_all_reads\\\": \\\"false\\\", \\\"otu\\\": {\\\"otu_map\\\": \\\"False\\\", \\\"__current_case__\\\": 1}}\", \"e_value\": \"\\\"1.0\\\"\", \"aligned_fastx\": \"{\\\"aligned_fastx_selector\\\": \\\"--fastx\\\", \\\"other\\\": \\\"true\\\", \\\"__current_case__\\\": 0}\", \"gap_ext\": \"\\\"2\\\"\"}", "id": 5, "tool_shed_repository": {"owner": "rnateam", "changeset_revision": "65c38d020fea", "name": "sortmerna", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "dfaecd0c-620e-4ff0-89ca-cd1af49795c6", "errors": null, "name": "Filter with SortMeRNA", "post_job_actions": {}, "label": "rRNA/rDNA selection", "inputs": [{"name": "sequencing_type", "description": "runtime parameter for tool Filter with SortMeRNA"}], "position": {"top": 998, "left": 964.5}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.5", "type": "tool"}, "6": {"tool_id": "toolshed.g2.bx.psu.edu/repos/bebatut/format_metaphlan2_output/format_metaphlan2_output/0.1.0", "tool_version": "0.1.0", "outputs": [{"type": "tabular", "name": "all_taxo_level_abundance_file"}, {"type": "tabular", "name": "kingdom_abundance_file"}, {"type": "tabular", "name": "phylum_abundance_file"}, {"type": "tabular", "name": "class_abundance_file"}, {"type": "tabular", "name": "order_abundance_file"}, {"type": "tabular", "name": "family_abundance_file"}, {"type": "tabular", "name": "genus_abundance_file"}, {"type": "tabular", "name": "species_abundance_file"}, {"type": "tabular", "name": "strains_abundance_file"}], "workflow_outputs": [], "input_connections": {"input_file": {"output_name": "output_file", "id": 4}}, "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "id": 6, "tool_shed_repository": {"owner": "bebatut", "changeset_revision": "2bfa9b200600", "name": "format_metaphlan2_output", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "be78f650-b4ec-4373-8e3a-d677aaed5e22", "errors": null, "name": "Format MetaPhlAn2", "post_job_actions": {}, "label": "Formatting for the different taxonomic levels", "inputs": [{"name": "input_file", "description": "runtime parameter for tool Format MetaPhlAn2"}], "position": {"top": 100, "left": 1263}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bebatut/format_metaphlan2_output/format_metaphlan2_output/0.1.0", "type": "tool"}, "7": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2krona/metaphlan2krona/2.6.0.0", "tool_version": "2.6.0.0", "outputs": [{"type": "tabular", "name": "krona"}], "workflow_outputs": [], "input_connections": {"profile": {"output_name": "output_file", "id": 4}}, "tool_state": "{\"profile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "id": 7, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "fdbd63e92b01", "name": "metaphlan2krona", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "5993071a-004b-4a52-8499-5705a6c26742", "errors": null, "name": "Format MetaPhlAn2", "post_job_actions": {}, "label": null, "inputs": [{"name": "profile", "description": "runtime parameter for tool Format MetaPhlAn2"}], "position": {"top": 431, "left": 1331}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2krona/metaphlan2krona/2.6.0.0", "type": "tool"}, "8": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.19", "tool_version": "0.19", "outputs": [{"type": "txt", "name": "tree"}, {"type": "txt", "name": "annotation"}], "workflow_outputs": [], "input_connections": {"lefse_input": {"output_name": "output_file", "id": 4}}, "tool_state": "{\"ftop\": \"\\\"\\\"\", \"background_clades\": \"\\\"\\\"\", \"max_clade_size\": \"\\\"200\\\"\", \"def_font_size\": \"\\\"10\\\"\", \"external_annotations\": \"\\\"\\\"\", \"annotation_legend_font_size\": \"\\\"10\\\"\", \"__page__\": null, \"skip_rows\": \"\\\"\\\"\", \"title\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"metadata_rows\": \"\\\"\\\"\", \"least_biomarkers\": \"\\\"\\\"\", \"min_clade_size\": \"\\\"20\\\"\", \"sperc\": \"\\\"\\\"\", \"fperc\": \"\\\"\\\"\", \"annotations\": \"\\\"\\\"\", \"lefse_input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"background_colors\": \"\\\"\\\"\", \"def_clade_size\": \"\\\"10\\\"\", \"stop\": \"\\\"\\\"\", \"sname_row\": \"\\\"0\\\"\", \"max_font_size\": \"\\\"12\\\"\", \"fname_row\": \"\\\"0\\\"\", \"abundance_threshold\": \"\\\"20.0\\\"\", \"title_font_size\": \"\\\"15\\\"\", \"input_lefse_output\": \"{\\\"input_lefse_output_test\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\", \"background_levels\": \"\\\"\\\"\", \"min_font_size\": \"\\\"8\\\"\", \"most_abundant\": \"\\\"\\\"\"}", "id": 8, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "ed1becc01910", "name": "export2graphlan", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "2b184419-ebe1-40d0-b404-9048e3cfd20c", "errors": null, "name": "Export to GraPhlAn", "post_job_actions": {}, "label": null, "inputs": [{"name": "lefse_input", "description": "runtime parameter for tool Export to GraPhlAn"}], "position": {"top": 545, "left": 1326}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.19", "type": "tool"}, "9": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/humann2/humann2/0.11.1.0", "tool_version": "0.11.1.0", "outputs": [{"type": "tsv", "name": "gene_families_tsv"}, {"type": "biom1", "name": "gene_families_biom"}, {"type": "tsv", "name": "pathcoverage_tsv"}, {"type": "biom1", "name": "pathcoverage_biom"}, {"type": "tsv", "name": "pathabundance_tsv"}, {"type": "biom1", "name": "pathabundance_biom"}], "workflow_outputs": [], "input_connections": {"input": {"output_name": "output_other", "id": 5}, "taxo_profile|taxonomic_profile": {"output_name": "output_file", "id": 4}}, "tool_state": "{\"adv\": \"{\\\"translated_query_coverage_threshold\\\": \\\"50.0\\\", \\\"translated_subject_coverage_threshold\\\": \\\"50.0\\\", \\\"prescreen_threshold\\\": \\\"0.01\\\", \\\"evalue\\\": \\\"1.0\\\", \\\"annotation_gene_index\\\": \\\"8\\\", \\\"minpath\\\": \\\"true\\\", \\\"id_mapping\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"identity_threshold\\\": \\\"50.0\\\", \\\"remove_statified_output\\\": \\\"false\\\", \\\"xipe\\\": \\\"false\\\", \\\"pick_frames\\\": \\\"true\\\", \\\"gap_fill\\\": \\\"true\\\", \\\"output_format\\\": \\\"tsv\\\", \\\"remove_column_description_output\\\": \\\"false\\\", \\\"output_max_dec\\\": \\\"10\\\"}\", \"__page__\": null, \"bypass\": \"{\\\"bypass_translated_search\\\": \\\"false\\\", \\\"bypass_nucleotide_search\\\": \\\"false\\\", \\\"bypass_prescreen\\\": \\\"false\\\", \\\"bypass_nucleotide_index\\\": \\\"false\\\"}\", \"translated_alignment\": \"\\\"diamond\\\"\", \"__rerun_remap_job_id__\": null, \"taxo_profile\": \"{\\\"taxonomic_profile_test\\\": \\\"true\\\", \\\"taxonomic_profile\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"pathways\": \"\\\"metacyc\\\"\", \"nucleotide_db\": \"{\\\"nucleotide_db_selector\\\": \\\"cached\\\", \\\"nucleotide_database\\\": \\\"chocophlan-full-2018-01-22\\\", \\\"__current_case__\\\": 0}\", \"search_mode\": \"\\\"uniref50\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"protein_db\": \"{\\\"protein_db_selector\\\": \\\"cached\\\", \\\"__current_case__\\\": 0, \\\"protein_database\\\": \\\"uniref-uniref50_diamond-2018-01-22\\\"}\"}", "id": 9, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "ca82f52681af", "name": "humann2", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "51a8b591-8fe0-43f7-ad38-0d2ea2c217d6", "errors": null, "name": "HUMAnN2", "post_job_actions": {}, "label": "Metabolic assignation", "inputs": [{"name": "adv", "description": "runtime parameter for tool HUMAnN2"}, {"name": "taxo_profile", "description": "runtime parameter for tool HUMAnN2"}, {"name": "input", "description": "runtime parameter for tool HUMAnN2"}], "position": {"top": 918, "left": 1237}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/humann2/humann2/0.11.1.0", "type": "tool"}, "10": {"tool_id": "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1", "tool_version": "2.6.1", "outputs": [{"type": "html", "name": "output"}], "workflow_outputs": [], "input_connections": {"type_of_data|input": {"output_name": "krona", "id": 7}}, "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"combine_inputs\": \"\\\"false\\\"\", \"type_of_data\": \"{\\\"input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"type_of_data_selector\\\": \\\"text\\\", \\\"__current_case__\\\": 1}\", \"root_name\": \"\\\"Root\\\"\"}", "id": 10, "tool_shed_repository": {"owner": "crs4", "changeset_revision": "d41b98e72c4c", "name": "taxonomy_krona_chart", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "705bc931-908a-459d-8d8a-5c6b14286151", "errors": null, "name": "Krona pie chart", "post_job_actions": {}, "label": "Visualisation (KRONA)", "inputs": [{"name": "type_of_data", "description": "runtime parameter for tool Krona pie chart"}], "position": {"top": 406, "left": 1606}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1", "type": "tool"}, "11": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.0.0.0", "tool_version": "1.0.0.0", "outputs": [{"type": "phyloxml", "name": "output_tree"}], "workflow_outputs": [], "input_connections": {"input_tree": {"output_name": "tree", "id": 8}, "annot": {"output_name": "annotation", "id": 8}}, "tool_state": "{\"input_tree\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"annot\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null}", "id": 11, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "5d6f8f0bef7c", "name": "graphlan_annotate", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "17c154d8-fbb8-4745-a5f6-62a5b653d0bf", "errors": null, "name": "Generation, personalization and annotation of tree", "post_job_actions": {}, "label": null, "inputs": [{"name": "input_tree", "description": "runtime parameter for tool Generation, personalization and annotation of tree"}, {"name": "annot", "description": "runtime parameter for tool Generation, personalization and annotation of tree"}], "position": {"top": 539, "left": 1582}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.0.0.0", "type": "tool"}, "12": {"tool_id": "toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.1.0", "tool_version": "0.1.0", "outputs": [{"type": "tabular", "name": "gene_families_output_file"}, {"type": "tabular", "name": "pathway_output_file"}], "workflow_outputs": [], "input_connections": {"metaphlan2_file": {"output_name": "output_file", "id": 4}, "humann2_file": {"output_name": "gene_families_tsv", "id": 9}}, "tool_state": "{\"metaphlan2_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"humann2_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"type\": \"\\\"gene_families\\\"\", \"__page__\": null}", "id": 12, "tool_shed_repository": {"owner": "bebatut", "changeset_revision": "31394a0c0242", "name": "combine_metaphlan2_humann2", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "ee12a2ef-1d55-43f1-b0a2-cbe005539b0d", "errors": null, "name": "Combine MetaPhlAn2 and HUMAnN2 outputs", "post_job_actions": {}, "label": "Combination of taxonomic and metabolic assignations for gene families", "inputs": [{"name": "metaphlan2_file", "description": "runtime parameter for tool Combine MetaPhlAn2 and HUMAnN2 outputs"}, {"name": "humann2_file", "description": "runtime parameter for tool Combine MetaPhlAn2 and HUMAnN2 outputs"}], "position": {"top": 686, "left": 1560.5}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.1.0", "type": "tool"}, "13": {"tool_id": "toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.1.0", "tool_version": "0.1.0", "outputs": [{"type": "tabular", "name": "gene_families_output_file"}, {"type": "tabular", "name": "pathway_output_file"}], "workflow_outputs": [], "input_connections": {"metaphlan2_file": {"output_name": "output_file", "id": 4}, "humann2_file": {"output_name": "pathabundance_tsv", "id": 9}}, "tool_state": "{\"metaphlan2_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"humann2_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"type\": \"\\\"gene_families\\\"\", \"__page__\": null}", "id": 13, "tool_shed_repository": {"owner": "bebatut", "changeset_revision": "31394a0c0242", "name": "combine_metaphlan2_humann2", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "5d19d8f9-2e6c-4506-a62a-636c242277a9", "errors": null, "name": "Combine MetaPhlAn2 and HUMAnN2 outputs", "post_job_actions": {}, "label": "Combination of taxonomic and metabolic assignations for pathways", "inputs": [{"name": "metaphlan2_file", "description": "runtime parameter for tool Combine MetaPhlAn2 and HUMAnN2 outputs"}, {"name": "humann2_file", "description": "runtime parameter for tool Combine MetaPhlAn2 and HUMAnN2 outputs"}], "position": {"top": 1137, "left": 1640.5}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.1.0", "type": "tool"}, "14": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/humann2_genefamilies_genus_level/humann2_genefamilies_genus_level/0.11.1.0", "tool_version": "0.11.1.0", "outputs": [{"type": "tsv", "name": "output"}], "workflow_outputs": [], "input_connections": {"input": {"output_name": "gene_families_tsv", "id": 9}}, "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}", "id": 14, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "5628423eb63e", "name": "humann2_genefamilies_genus_level", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "5a93decf-fca2-419e-a979-c5ab7d51d362", "errors": null, "name": "Create a genus level gene families file", "post_job_actions": {}, "label": null, "inputs": [{"name": "input", "description": "runtime parameter for tool Create a genus level gene families file"}], "position": {"top": 785, "left": 1866.5}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/humann2_genefamilies_genus_level/humann2_genefamilies_genus_level/0.11.1.0", "type": "tool"}, "15": {"tool_id": "toolshed.g2.bx.psu.edu/repos/bebatut/group_humann2_uniref_abundances_to_go/group_humann2_uniref_abundances_to_go/1.2.0", "tool_version": "1.2.0", "outputs": [{"type": "tabular", "name": "molecular_function_abundance"}, {"type": "tabular", "name": "biological_process_abundance"}, {"type": "tabular", "name": "cellular_component_abundance"}], "workflow_outputs": [], "input_connections": {"humann2_gene_families_abundance": {"output_name": "gene_families_tsv", "id": 9}}, "tool_state": "{\"__page__\": null, \"gene_ontology\": \"{\\\"gene_ontology_test\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\", \"slim_gene_ontology\": \"{\\\"slim_gene_ontology_test\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\", \"humann2_gene_families_abundance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"uniref50_go\": \"{\\\"uniref50_go_test\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\"}", "id": 15, "tool_shed_repository": {"owner": "bebatut", "changeset_revision": "cad28d7b49d2", "name": "group_humann2_uniref_abundances_to_go", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "c5c483ec-a212-4742-9da3-544ad53108b7", "errors": null, "name": "Group abundances", "post_job_actions": {}, "label": "Grouping to high level GO Slim terms", "inputs": [{"name": "humann2_gene_families_abundance", "description": "runtime parameter for tool Group abundances"}], "position": {"top": 906, "left": 1868}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bebatut/group_humann2_uniref_abundances_to_go/group_humann2_uniref_abundances_to_go/1.2.0", "type": "tool"}, "16": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.0.0.0", "tool_version": "1.0.0.0", "outputs": [{"type": "png", "name": "png_output_image"}, {"type": "pdf", "name": "pdf_output_image"}, {"type": "ps", "name": "ps_output_image"}, {"type": "eps", "name": "eps_output_image"}, {"type": "svg", "name": "svg_output_image"}], "workflow_outputs": [], "input_connections": {"input_tree": {"output_name": "output_tree", "id": 11}}, "tool_state": "{\"__page__\": null, \"input_tree\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"pad\": \"\\\"\\\"\", \"image_format\": \"{\\\"dpi\\\": \\\"\\\", \\\"__current_case__\\\": 0, \\\"format\\\": \\\"png\\\"}\", \"size\": \"\\\"7\\\"\"}", "id": 16, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "8f62f666dcb6", "name": "graphlan", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "324857c9-bfd9-4fcb-8183-f7dcab4651a3", "errors": null, "name": "GraPhlAn", "post_job_actions": {}, "label": "Visualisation (GraPhlAn)", "inputs": [{"name": "input_tree", "description": "runtime parameter for tool GraPhlAn"}], "position": {"top": 510, "left": 1928}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.0.0.0", "type": "tool"}}, "annotation": "", "a_galaxy_workflow": "true"}, "workflow_outputs": [], "input_connections": {"Raw reads": {"input_subworkflow_step_id": 0, "output_name": "outputJoined", "id": 2}}, "id": 3, "uuid": "2a7b85ac-f160-4db9-bf9e-14cef1cfe53a", "name": "Shotgun workflow", "label": null, "position": {"top": 275.5, "left": 703}, "annotation": "", "type": "subworkflow"}}, "annotation": "", "a_galaxy_workflow": "true"} \ No newline at end of file diff --git a/config/workflows/shotgun_workflow_pe_collection.ga b/config/workflows/shotgun_workflow_pe_collection.ga new file mode 100644 index 0000000..a46bec1 --- /dev/null +++ b/config/workflows/shotgun_workflow_pe_collection.ga @@ -0,0 +1 @@ +{"uuid": "70b9a0a0-a3db-488b-bd85-83401ddec5fd", "tags": [], "format-version": "0.1", "name": "Shotgun workflow for paired-end data collection", "steps": {"0": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{\"collection_type\": \"list\"}", "id": 0, "uuid": "2763a19d-d18c-4bd1-9538-ed9990e904fc", "errors": null, "name": "Input dataset collection", "label": "R1", "inputs": [], "position": {"top": 241.5, "left": 306}, "annotation": "", "content_id": null, "type": "data_collection_input"}, "1": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{\"collection_type\": \"list\"}", "id": 1, "uuid": "ccc9d2d6-cbbe-4f9e-bd24-995e1ebbdaca", "errors": null, "name": "Input dataset collection", "label": "R2", "inputs": [], "position": {"top": 331.5, "left": 307}, "annotation": "", "content_id": null, "type": "data_collection_input"}, "2": {"tool_id": "964b37715ec9bd22", "inputs": [], "outputs": [], "subworkflow": {"uuid": "90c04ef0-3c34-4e5a-9a98-7482f35e3ec2", "tags": "", "format-version": "0.1", "name": "Shotgun workflow for paired-end data", "steps": {"0": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{}", "id": 0, "uuid": "da4d90df-bfaf-43be-bb68-82b102d7d492", "errors": null, "name": "Input dataset", "label": "R1 reads", "inputs": [], "position": {"top": 165.5, "left": 143.5}, "annotation": "", "content_id": null, "type": "data_input"}, "1": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{}", "id": 1, "uuid": "b9a10a93-0e4c-443c-82d4-6d1df1885464", "errors": null, "name": "Input dataset", "label": "R2 reads", "inputs": [], "position": {"top": 286.5, "left": 143.5}, "annotation": "", "content_id": null, "type": "data_input"}, "2": {"tool_id": "toolshed.g2.bx.psu.edu/repos/lparsons/fastq_join/fastq_join/1.1.2-806.1", "tool_version": "1.1.2-806.1", "outputs": [{"type": "fastqsanger", "name": "outputJoined"}, {"type": "fastqsanger", "name": "outputUnmatched1"}, {"type": "fastqsanger", "name": "outputUnmatched2"}, {"type": "tabular", "name": "outputStitchLengthReport"}], "workflow_outputs": [], "input_connections": {"input_type|read2": {"output_name": "output", "id": 1}, "input_type|read1": {"output_name": "output", "id": 0}}, "tool_state": "{\"__page__\": null, \"stitchLengthReport\": \"\\\"false\\\"\", \"input_type\": \"{\\\"read1\\\": {\\\"values\\\": [{\\\"src\\\": \\\"hda\\\", \\\"id\\\": 50}]}, \\\"read2\\\": {\\\"values\\\": [{\\\"src\\\": \\\"hda\\\", \\\"id\\\": 50}]}, \\\"__current_case__\\\": 0, \\\"input_type_selector\\\": \\\"paired\\\"}\", \"__rerun_remap_job_id__\": null, \"splitChar\": \"\\\" \\\"\", \"minOverlap\": \"\\\"6\\\"\", \"pctMaxDiff\": \"\\\"8.0\\\"\"}", "id": 2, "tool_shed_repository": {"owner": "lparsons", "changeset_revision": "8ec3dfde378b", "name": "fastq_join", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "a8a601f3-3836-4865-9ec3-03c3f29007d0", "errors": null, "name": "fastq-join", "post_job_actions": {}, "label": null, "inputs": [], "position": {"top": 211.5, "left": 368.5}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/lparsons/fastq_join/fastq_join/1.1.2-806.1", "type": "tool"}, "3": {"tool_id": "5969b1f7201f12ae", "inputs": [], "outputs": [], "subworkflow": {"uuid": "8aee346b-9de0-4b5d-826d-0cc1d110adc2", "tags": "", "format-version": "0.1", "name": "Shotgun workflow", "steps": {"0": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{}", "id": 0, "uuid": "443cdeb2-5918-423f-8821-1bf732dc678c", "errors": null, "name": "Input dataset", "label": "Raw reads", "inputs": [], "position": {"top": 689, "left": 207}, "annotation": "", "content_id": null, "type": "data_input"}, "1": {"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71", "tool_version": "0.71", "outputs": [{"type": "html", "name": "html_file"}, {"type": "txt", "name": "text_file"}], "workflow_outputs": [], "input_connections": {"input_file": {"output_name": "output", "id": 0}}, "tool_state": "{\"__page__\": null, \"contaminants\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"limits\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "id": 1, "tool_shed_repository": {"owner": "devteam", "changeset_revision": "ff9530579d1f", "name": "fastqc", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "f9aa307f-2e7c-4ebd-948d-011ffcfd5f26", "errors": null, "name": "FastQC", "post_job_actions": {}, "label": "Quality control", "inputs": [{"name": "contaminants", "description": "runtime parameter for tool FastQC"}, {"name": "limits", "description": "runtime parameter for tool FastQC"}, {"name": "input_file", "description": "runtime parameter for tool FastQC"}], "position": {"top": 609, "left": 404}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71", "type": "tool"}, "2": {"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1", "tool_version": "0.4.3.1", "outputs": [{"type": "input", "name": "trimmed_reads_paired_collection"}, {"type": "input", "name": "trimmed_reads_unpaired_collection"}, {"type": "input", "name": "trimmed_reads_single"}, {"type": "input", "name": "trimmed_reads_pair1"}, {"type": "input", "name": "trimmed_reads_pair2"}, {"type": "input", "name": "unpaired_reads_1"}, {"type": "input", "name": "unpaired_reads_2"}, {"type": "txt", "name": "report_file"}], "workflow_outputs": [], "input_connections": {"singlePaired|input_singles": {"output_name": "output", "id": 0}}, "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"params\": \"{\\\"settingsType\\\": \\\"default\\\", \\\"__current_case__\\\": 0}\", \"rrbs\": \"{\\\"settingsType\\\": \\\"default\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"three_prime_clip_R1\\\": \\\"\\\", \\\"trimming\\\": {\\\"trimming_select\\\": \\\"\\\", \\\"__current_case__\\\": 0}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0, \\\"input_singles\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\"}", "id": 2, "tool_shed_repository": {"owner": "bgruening", "changeset_revision": "949f01671246", "name": "trim_galore", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "0533b5d9-7a59-438c-a74b-0b7687f481ea", "errors": null, "name": "Trim Galore!", "post_job_actions": {}, "label": "Trimming", "inputs": [{"name": "singlePaired", "description": "runtime parameter for tool Trim Galore!"}], "position": {"top": 831, "left": 411}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1", "type": "tool"}, "3": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_dereplication/1.9.7.0", "tool_version": "1.9.7.0", "outputs": [{"type": "fasta", "name": "outfile"}, {"type": "fasta", "name": "uc_outfile"}], "workflow_outputs": [], "input_connections": {"infile": {"output_name": "trimmed_reads_single", "id": 2}}, "tool_state": "{\"sizein\": \"\\\"false\\\"\", \"__page__\": null, \"maxuniquesize\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"minuniquesize\": \"\\\"\\\"\", \"topn\": \"\\\"\\\"\", \"strand\": \"\\\"plus\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"sizeout\": \"\\\"false\\\"\", \"uc\": \"\\\"false\\\"\"}", "id": 3, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "576963db5f1b", "name": "vsearch", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "98dc5416-f149-4e69-874c-48c4a8a67b09", "errors": null, "name": "VSearch dereplication", "post_job_actions": {}, "label": "Dereplication", "inputs": [{"name": "infile", "description": "runtime parameter for tool VSearch dereplication"}], "position": {"top": 913, "left": 706}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_dereplication/1.9.7.0", "type": "tool"}, "4": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2/metaphlan2/2.6.0.0", "tool_version": "2.6.0.0", "outputs": [{"type": "tabular", "name": "output_file"}, {"type": "sam", "name": "sam_output_file"}, {"type": "biom", "name": "biom_output_file"}], "workflow_outputs": [], "input_connections": {"input_file": {"output_name": "outfile", "id": 3}}, "tool_state": "{\"min_cu_len\": \"\\\"2000\\\"\", \"min_alignment_len\": \"\\\"0\\\"\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null, \"ignore_eukaryotes\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"db\": \"{\\\"db_selector\\\": \\\"cached\\\", \\\"cached_db\\\": \\\"mpa_v20_m200\\\", \\\"__current_case__\\\": 0}\", \"stat_q\": \"\\\"0.1\\\"\", \"ignore_viruses\": \"\\\"true\\\"\", \"ignore_archaea\": \"\\\"true\\\"\", \"analysis_type\": \"{\\\"tax_lev\\\": \\\"a\\\", \\\"analysis_type_select\\\": \\\"rel_ab\\\", \\\"__current_case__\\\": 0}\", \"ignore_bacteria\": \"\\\"true\\\"\"}", "id": 4, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "8c82c4d90cc6", "name": "metaphlan2", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "7281de8c-c5df-48dd-841a-80c468b5fe75", "errors": null, "name": "MetaPhlAn2", "post_job_actions": {}, "label": "Taxonomic assignation", "inputs": [{"name": "input_file", "description": "runtime parameter for tool MetaPhlAn2"}], "position": {"top": 698, "left": 982}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2/metaphlan2/2.6.0.0", "type": "tool"}, "5": {"tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.5", "tool_version": "2.1b.5", "outputs": [{"type": "input", "name": "output_fastx"}, {"type": "fastq", "name": "output_paired_fastx"}, {"type": "fastq", "name": "aligned_forward"}, {"type": "fastq", "name": "aligned_reverse"}, {"type": "input", "name": "output_other"}, {"type": "fastq", "name": "output_paired_other"}, {"type": "fastq", "name": "unaligned_forward"}, {"type": "fastq", "name": "unaligned_reverse"}, {"type": "bam", "name": "output_bam"}, {"type": "tabular", "name": "output_blast"}, {"type": "txt", "name": "output_biom"}, {"type": "input", "name": "output_de_novo"}, {"type": "txt", "name": "output_log"}], "workflow_outputs": [], "input_connections": {"sequencing_type|reads": {"output_name": "outfile", "id": 3}}, "tool_state": "{\"__page__\": null, \"strand_search\": \"\\\"\\\"\", \"aligned_sam\": \"{\\\"aligned_sam_selector\\\": \\\"--sam\\\", \\\"sq\\\": \\\"false\\\", \\\"__current_case__\\\": 0}\", \"log\": \"\\\"false\\\"\", \"input_reads\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"mismatch\": \"\\\"-3\\\"\", \"sequencing_type\": \"{\\\"reads\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sequencing_type_selector\\\": \\\"not_paired\\\", \\\"__current_case__\\\": 0}\", \"ambiguous_letter\": \"\\\"-3\\\"\", \"aligned_blast\": \"{\\\"__current_case__\\\": 1, \\\"aligned_blast_selector\\\": \\\"\\\"}\", \"databases_type\": \"{\\\"databases_selector\\\": \\\"cached\\\", \\\"input_databases\\\": [\\\"2.1b-silva-bac-23s-id98\\\", \\\"2.1b-silva-bac-16s-id90\\\", \\\"2.1b-silva-euk-28s-id98\\\", \\\"2.1b-rfam-5.8s-database-id98\\\", \\\"2.1b-silva-euk-18s-id95\\\", \\\"2.1b-silva-arc-16s-id95\\\", \\\"2.1b-silva-arc-23s-id98\\\", \\\"2.1b-rfam-5s-database-id98\\\"], \\\"__current_case__\\\": 0}\", \"match\": \"\\\"2\\\"\", \"gap_open\": \"\\\"5\\\"\", \"report\": \"{\\\"report_best\\\": {\\\"report_best_min_lis\\\": \\\"2\\\", \\\"__current_case__\\\": 0, \\\"report_best_type\\\": \\\"1\\\"}, \\\"report_type\\\": \\\"best\\\", \\\"__current_case__\\\": 1, \\\"blast\\\": {\\\"blast_output\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"print_all_reads\\\": \\\"false\\\", \\\"otu\\\": {\\\"otu_map\\\": \\\"False\\\", \\\"__current_case__\\\": 1}}\", \"e_value\": \"\\\"1.0\\\"\", \"aligned_fastx\": \"{\\\"aligned_fastx_selector\\\": \\\"--fastx\\\", \\\"other\\\": \\\"true\\\", \\\"__current_case__\\\": 0}\", \"gap_ext\": \"\\\"2\\\"\"}", "id": 5, "tool_shed_repository": {"owner": "rnateam", "changeset_revision": "65c38d020fea", "name": "sortmerna", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "dfaecd0c-620e-4ff0-89ca-cd1af49795c6", "errors": null, "name": "Filter with SortMeRNA", "post_job_actions": {}, "label": "rRNA/rDNA selection", "inputs": [{"name": "sequencing_type", "description": "runtime parameter for tool Filter with SortMeRNA"}], "position": {"top": 998, "left": 964.5}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.5", "type": "tool"}, "6": {"tool_id": "toolshed.g2.bx.psu.edu/repos/bebatut/format_metaphlan2_output/format_metaphlan2_output/0.1.0", "tool_version": "0.1.0", "outputs": [{"type": "tabular", "name": "all_taxo_level_abundance_file"}, {"type": "tabular", "name": "kingdom_abundance_file"}, {"type": "tabular", "name": "phylum_abundance_file"}, {"type": "tabular", "name": "class_abundance_file"}, {"type": "tabular", "name": "order_abundance_file"}, {"type": "tabular", "name": "family_abundance_file"}, {"type": "tabular", "name": "genus_abundance_file"}, {"type": "tabular", "name": "species_abundance_file"}, {"type": "tabular", "name": "strains_abundance_file"}], "workflow_outputs": [], "input_connections": {"input_file": {"output_name": "output_file", "id": 4}}, "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "id": 6, "tool_shed_repository": {"owner": "bebatut", "changeset_revision": "2bfa9b200600", "name": "format_metaphlan2_output", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "be78f650-b4ec-4373-8e3a-d677aaed5e22", "errors": null, "name": "Format MetaPhlAn2", "post_job_actions": {}, "label": "Formatting for the different taxonomic levels", "inputs": [{"name": "input_file", "description": "runtime parameter for tool Format MetaPhlAn2"}], "position": {"top": 100, "left": 1263}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bebatut/format_metaphlan2_output/format_metaphlan2_output/0.1.0", "type": "tool"}, "7": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2krona/metaphlan2krona/2.6.0.0", "tool_version": "2.6.0.0", "outputs": [{"type": "tabular", "name": "krona"}], "workflow_outputs": [], "input_connections": {"profile": {"output_name": "output_file", "id": 4}}, "tool_state": "{\"profile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "id": 7, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "fdbd63e92b01", "name": "metaphlan2krona", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "5993071a-004b-4a52-8499-5705a6c26742", "errors": null, "name": "Format MetaPhlAn2", "post_job_actions": {}, "label": null, "inputs": [{"name": "profile", "description": "runtime parameter for tool Format MetaPhlAn2"}], "position": {"top": 431, "left": 1331}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2krona/metaphlan2krona/2.6.0.0", "type": "tool"}, "8": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.19", "tool_version": "0.19", "outputs": [{"type": "txt", "name": "tree"}, {"type": "txt", "name": "annotation"}], "workflow_outputs": [], "input_connections": {"lefse_input": {"output_name": "output_file", "id": 4}}, "tool_state": "{\"ftop\": \"\\\"\\\"\", \"background_clades\": \"\\\"\\\"\", \"max_clade_size\": \"\\\"200\\\"\", \"def_font_size\": \"\\\"10\\\"\", \"external_annotations\": \"\\\"\\\"\", \"annotation_legend_font_size\": \"\\\"10\\\"\", \"__page__\": null, \"skip_rows\": \"\\\"\\\"\", \"title\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"metadata_rows\": \"\\\"\\\"\", \"least_biomarkers\": \"\\\"\\\"\", \"min_clade_size\": \"\\\"20\\\"\", \"sperc\": \"\\\"\\\"\", \"fperc\": \"\\\"\\\"\", \"annotations\": \"\\\"\\\"\", \"lefse_input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"background_colors\": \"\\\"\\\"\", \"def_clade_size\": \"\\\"10\\\"\", \"stop\": \"\\\"\\\"\", \"sname_row\": \"\\\"0\\\"\", \"max_font_size\": \"\\\"12\\\"\", \"fname_row\": \"\\\"0\\\"\", \"abundance_threshold\": \"\\\"20.0\\\"\", \"title_font_size\": \"\\\"15\\\"\", \"input_lefse_output\": \"{\\\"input_lefse_output_test\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\", \"background_levels\": \"\\\"\\\"\", \"min_font_size\": \"\\\"8\\\"\", \"most_abundant\": \"\\\"\\\"\"}", "id": 8, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "ed1becc01910", "name": "export2graphlan", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "2b184419-ebe1-40d0-b404-9048e3cfd20c", "errors": null, "name": "Export to GraPhlAn", "post_job_actions": {}, "label": null, "inputs": [{"name": "lefse_input", "description": "runtime parameter for tool Export to GraPhlAn"}], "position": {"top": 545, "left": 1326}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.19", "type": "tool"}, "9": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/humann2/humann2/0.11.1.0", "tool_version": "0.11.1.0", "outputs": [{"type": "tsv", "name": "gene_families_tsv"}, {"type": "biom1", "name": "gene_families_biom"}, {"type": "tsv", "name": "pathcoverage_tsv"}, {"type": "biom1", "name": "pathcoverage_biom"}, {"type": "tsv", "name": "pathabundance_tsv"}, {"type": "biom1", "name": "pathabundance_biom"}], "workflow_outputs": [], "input_connections": {"input": {"output_name": "output_other", "id": 5}, "taxo_profile|taxonomic_profile": {"output_name": "output_file", "id": 4}}, "tool_state": "{\"adv\": \"{\\\"translated_query_coverage_threshold\\\": \\\"50.0\\\", \\\"translated_subject_coverage_threshold\\\": \\\"50.0\\\", \\\"prescreen_threshold\\\": \\\"0.01\\\", \\\"evalue\\\": \\\"1.0\\\", \\\"annotation_gene_index\\\": \\\"8\\\", \\\"minpath\\\": \\\"true\\\", \\\"id_mapping\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"identity_threshold\\\": \\\"50.0\\\", \\\"remove_statified_output\\\": \\\"false\\\", \\\"xipe\\\": \\\"false\\\", \\\"pick_frames\\\": \\\"true\\\", \\\"gap_fill\\\": \\\"true\\\", \\\"output_format\\\": \\\"tsv\\\", \\\"remove_column_description_output\\\": \\\"false\\\", \\\"output_max_dec\\\": \\\"10\\\"}\", \"__page__\": null, \"bypass\": \"{\\\"bypass_translated_search\\\": \\\"false\\\", \\\"bypass_nucleotide_search\\\": \\\"false\\\", \\\"bypass_prescreen\\\": \\\"false\\\", \\\"bypass_nucleotide_index\\\": \\\"false\\\"}\", \"translated_alignment\": \"\\\"diamond\\\"\", \"__rerun_remap_job_id__\": null, \"taxo_profile\": \"{\\\"taxonomic_profile_test\\\": \\\"true\\\", \\\"taxonomic_profile\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"pathways\": \"\\\"metacyc\\\"\", \"nucleotide_db\": \"{\\\"nucleotide_db_selector\\\": \\\"cached\\\", \\\"nucleotide_database\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"search_mode\": \"\\\"uniref50\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"protein_db\": \"{\\\"protein_db_selector\\\": \\\"cached\\\", \\\"__current_case__\\\": 0, \\\"protein_database\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\"}", "id": 9, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "ca82f52681af", "name": "humann2", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "51a8b591-8fe0-43f7-ad38-0d2ea2c217d6", "errors": null, "name": "HUMAnN2", "post_job_actions": {}, "label": "Metabolic assignation", "inputs": [{"name": "adv", "description": "runtime parameter for tool HUMAnN2"}, {"name": "taxo_profile", "description": "runtime parameter for tool HUMAnN2"}, {"name": "nucleotide_db", "description": "runtime parameter for tool HUMAnN2"}, {"name": "input", "description": "runtime parameter for tool HUMAnN2"}, {"name": "protein_db", "description": "runtime parameter for tool HUMAnN2"}], "position": {"top": 918, "left": 1237}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/humann2/humann2/0.11.1.0", "type": "tool"}, "10": {"tool_id": "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1", "tool_version": "2.6.1", "outputs": [{"type": "html", "name": "output"}], "workflow_outputs": [], "input_connections": {"type_of_data|input": {"output_name": "krona", "id": 7}}, "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"combine_inputs\": \"\\\"false\\\"\", \"type_of_data\": \"{\\\"input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"type_of_data_selector\\\": \\\"text\\\", \\\"__current_case__\\\": 1}\", \"root_name\": \"\\\"Root\\\"\"}", "id": 10, "tool_shed_repository": {"owner": "crs4", "changeset_revision": "d41b98e72c4c", "name": "taxonomy_krona_chart", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "705bc931-908a-459d-8d8a-5c6b14286151", "errors": null, "name": "Krona pie chart", "post_job_actions": {}, "label": "Visualisation (KRONA)", "inputs": [{"name": "type_of_data", "description": "runtime parameter for tool Krona pie chart"}], "position": {"top": 406, "left": 1606}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1", "type": "tool"}, "11": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.0.0.0", "tool_version": "1.0.0.0", "outputs": [{"type": "phyloxml", "name": "output_tree"}], "workflow_outputs": [], "input_connections": {"input_tree": {"output_name": "tree", "id": 8}, "annot": {"output_name": "annotation", "id": 8}}, "tool_state": "{\"input_tree\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"annot\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null}", "id": 11, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "5d6f8f0bef7c", "name": "graphlan_annotate", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "17c154d8-fbb8-4745-a5f6-62a5b653d0bf", "errors": null, "name": "Generation, personalization and annotation of tree", "post_job_actions": {}, "label": null, "inputs": [{"name": "input_tree", "description": "runtime parameter for tool Generation, personalization and annotation of tree"}, {"name": "annot", "description": "runtime parameter for tool Generation, personalization and annotation of tree"}], "position": {"top": 539, "left": 1582}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.0.0.0", "type": "tool"}, "12": {"tool_id": "toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.1.0", "tool_version": "0.1.0", "outputs": [{"type": "tabular", "name": "gene_families_output_file"}, {"type": "tabular", "name": "pathway_output_file"}], "workflow_outputs": [], "input_connections": {"metaphlan2_file": {"output_name": "output_file", "id": 4}, "humann2_file": {"output_name": "gene_families_tsv", "id": 9}}, "tool_state": "{\"metaphlan2_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"humann2_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"type\": \"\\\"gene_families\\\"\", \"__page__\": null}", "id": 12, "tool_shed_repository": {"owner": "bebatut", "changeset_revision": "31394a0c0242", "name": "combine_metaphlan2_humann2", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "ee12a2ef-1d55-43f1-b0a2-cbe005539b0d", "errors": null, "name": "Combine MetaPhlAn2 and HUMAnN2 outputs", "post_job_actions": {}, "label": "Combination of taxonomic and metabolic assignations for gene families", "inputs": [{"name": "metaphlan2_file", "description": "runtime parameter for tool Combine MetaPhlAn2 and HUMAnN2 outputs"}, {"name": "humann2_file", "description": "runtime parameter for tool Combine MetaPhlAn2 and HUMAnN2 outputs"}], "position": {"top": 686, "left": 1560.5}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.1.0", "type": "tool"}, "13": {"tool_id": "toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.1.0", "tool_version": "0.1.0", "outputs": [{"type": "tabular", "name": "gene_families_output_file"}, {"type": "tabular", "name": "pathway_output_file"}], "workflow_outputs": [], "input_connections": {"metaphlan2_file": {"output_name": "output_file", "id": 4}, "humann2_file": {"output_name": "pathabundance_tsv", "id": 9}}, "tool_state": "{\"metaphlan2_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"humann2_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"type\": \"\\\"gene_families\\\"\", \"__page__\": null}", "id": 13, "tool_shed_repository": {"owner": "bebatut", "changeset_revision": "31394a0c0242", "name": "combine_metaphlan2_humann2", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "5d19d8f9-2e6c-4506-a62a-636c242277a9", "errors": null, "name": "Combine MetaPhlAn2 and HUMAnN2 outputs", "post_job_actions": {}, "label": "Combination of taxonomic and metabolic assignations for pathways", "inputs": [{"name": "metaphlan2_file", "description": "runtime parameter for tool Combine MetaPhlAn2 and HUMAnN2 outputs"}, {"name": "humann2_file", "description": "runtime parameter for tool Combine MetaPhlAn2 and HUMAnN2 outputs"}], "position": {"top": 1137, "left": 1640.5}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.1.0", "type": "tool"}, "14": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/humann2_genefamilies_genus_level/humann2_genefamilies_genus_level/0.11.1.0", "tool_version": "0.11.1.0", "outputs": [{"type": "tsv", "name": "output"}], "workflow_outputs": [], "input_connections": {"input": {"output_name": "gene_families_tsv", "id": 9}}, "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}", "id": 14, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "5628423eb63e", "name": "humann2_genefamilies_genus_level", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "5a93decf-fca2-419e-a979-c5ab7d51d362", "errors": null, "name": "Create a genus level gene families file", "post_job_actions": {}, "label": null, "inputs": [{"name": "input", "description": "runtime parameter for tool Create a genus level gene families file"}], "position": {"top": 785, "left": 1866.5}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/humann2_genefamilies_genus_level/humann2_genefamilies_genus_level/0.11.1.0", "type": "tool"}, "15": {"tool_id": "toolshed.g2.bx.psu.edu/repos/bebatut/group_humann2_uniref_abundances_to_go/group_humann2_uniref_abundances_to_go/1.2.0", "tool_version": "1.2.0", "outputs": [{"type": "tabular", "name": "molecular_function_abundance"}, {"type": "tabular", "name": "biological_process_abundance"}, {"type": "tabular", "name": "cellular_component_abundance"}], "workflow_outputs": [], "input_connections": {"humann2_gene_families_abundance": {"output_name": "gene_families_tsv", "id": 9}}, "tool_state": "{\"__page__\": null, \"gene_ontology\": \"{\\\"gene_ontology_test\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\", \"slim_gene_ontology\": \"{\\\"slim_gene_ontology_test\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\", \"humann2_gene_families_abundance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"uniref50_go\": \"{\\\"uniref50_go_test\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\"}", "id": 15, "tool_shed_repository": {"owner": "bebatut", "changeset_revision": "cad28d7b49d2", "name": "group_humann2_uniref_abundances_to_go", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "c5c483ec-a212-4742-9da3-544ad53108b7", "errors": null, "name": "Group abundances", "post_job_actions": {}, "label": "Grouping to high level GO Slim terms", "inputs": [{"name": "humann2_gene_families_abundance", "description": "runtime parameter for tool Group abundances"}], "position": {"top": 906, "left": 1868}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bebatut/group_humann2_uniref_abundances_to_go/group_humann2_uniref_abundances_to_go/1.2.0", "type": "tool"}, "16": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.0.0.0", "tool_version": "1.0.0.0", "outputs": [{"type": "png", "name": "png_output_image"}, {"type": "pdf", "name": "pdf_output_image"}, {"type": "ps", "name": "ps_output_image"}, {"type": "eps", "name": "eps_output_image"}, {"type": "svg", "name": "svg_output_image"}], "workflow_outputs": [], "input_connections": {"input_tree": {"output_name": "output_tree", "id": 11}}, "tool_state": "{\"__page__\": null, \"input_tree\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"pad\": \"\\\"\\\"\", \"image_format\": \"{\\\"dpi\\\": \\\"\\\", \\\"__current_case__\\\": 0, \\\"format\\\": \\\"png\\\"}\", \"size\": \"\\\"7\\\"\"}", "id": 16, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "8f62f666dcb6", "name": "graphlan", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "324857c9-bfd9-4fcb-8183-f7dcab4651a3", "errors": null, "name": "GraPhlAn", "post_job_actions": {}, "label": "Visualisation (GraPhlAn)", "inputs": [{"name": "input_tree", "description": "runtime parameter for tool GraPhlAn"}], "position": {"top": 510, "left": 1928}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.0.0.0", "type": "tool"}}, "annotation": "", "a_galaxy_workflow": "true"}, "workflow_outputs": [], "input_connections": {"Raw reads": {"input_subworkflow_step_id": 0, "output_name": "outputJoined", "id": 2}}, "id": 3, "uuid": "5da78085-b5a7-42b4-9557-18d55bda142c", "name": "Shotgun workflow", "label": null, "position": {"top": 257.5, "left": 672.5}, "annotation": "", "type": "subworkflow"}}, "annotation": "", "a_galaxy_workflow": "true"}, "workflow_outputs": [], "input_connections": {"R1 reads": {"input_subworkflow_step_id": 0, "output_name": "output", "id": 0}, "R2 reads": {"input_subworkflow_step_id": 1, "output_name": "output", "id": 1}}, "id": 2, "uuid": "94f8b490-0e3a-471e-bd3f-f3ff3b680f28", "name": "Shotgun workflow for paired-end data", "label": null, "position": {"top": 328.5, "left": 629}, "annotation": "", "type": "subworkflow"}}, "annotation": "", "a_galaxy_workflow": "true"} \ No newline at end of file diff --git a/config/workflows/shotgun_workflow_se_collection.ga b/config/workflows/shotgun_workflow_se_collection.ga new file mode 100644 index 0000000..3d9d902 --- /dev/null +++ b/config/workflows/shotgun_workflow_se_collection.ga @@ -0,0 +1 @@ +{"uuid": "23940779-e2af-43f6-a8eb-ff58debd396b", "tags": [], "format-version": "0.1", "name": "Shotgun workflow for single-end data collection", "steps": {"0": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{\"collection_type\": \"list\"}", "id": 0, "uuid": "679c7cd0-50b7-4bab-ac8d-52b2ff4763e0", "errors": null, "name": "Input dataset collection", "label": "Single-end collection", "inputs": [], "position": {"top": 315.5, "left": 200}, "annotation": "", "content_id": null, "type": "data_collection_input"}, "1": {"tool_id": "c385e49b9fe1853c", "inputs": [], "outputs": [], "subworkflow": {"uuid": "a07c681b-a9c1-472e-bd7a-e5e4bdd736be", "tags": "", "format-version": "0.1", "name": "Shotgun workflow", "steps": {"0": {"tool_id": null, "tool_version": null, "outputs": [], "workflow_outputs": [], "input_connections": {}, "tool_state": "{}", "id": 0, "uuid": "443cdeb2-5918-423f-8821-1bf732dc678c", "errors": null, "name": "Input dataset", "label": "Raw reads", "inputs": [], "position": {"top": 689, "left": 207}, "annotation": "", "content_id": null, "type": "data_input"}, "1": {"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71", "tool_version": "0.71", "outputs": [{"type": "html", "name": "html_file"}, {"type": "txt", "name": "text_file"}], "workflow_outputs": [], "input_connections": {"input_file": {"output_name": "output", "id": 0}}, "tool_state": "{\"__page__\": null, \"contaminants\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"limits\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "id": 1, "tool_shed_repository": {"owner": "devteam", "changeset_revision": "ff9530579d1f", "name": "fastqc", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "f9aa307f-2e7c-4ebd-948d-011ffcfd5f26", "errors": null, "name": "FastQC", "post_job_actions": {}, "label": "Quality control", "inputs": [{"name": "contaminants", "description": "runtime parameter for tool FastQC"}, {"name": "limits", "description": "runtime parameter for tool FastQC"}, {"name": "input_file", "description": "runtime parameter for tool FastQC"}], "position": {"top": 609, "left": 404}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71", "type": "tool"}, "2": {"tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1", "tool_version": "0.4.3.1", "outputs": [{"type": "input", "name": "trimmed_reads_paired_collection"}, {"type": "input", "name": "trimmed_reads_unpaired_collection"}, {"type": "input", "name": "trimmed_reads_single"}, {"type": "input", "name": "trimmed_reads_pair1"}, {"type": "input", "name": "trimmed_reads_pair2"}, {"type": "input", "name": "unpaired_reads_1"}, {"type": "input", "name": "unpaired_reads_2"}, {"type": "txt", "name": "report_file"}], "workflow_outputs": [], "input_connections": {"singlePaired|input_singles": {"output_name": "output", "id": 0}}, "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"params\": \"{\\\"settingsType\\\": \\\"default\\\", \\\"__current_case__\\\": 0}\", \"rrbs\": \"{\\\"settingsType\\\": \\\"default\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"three_prime_clip_R1\\\": \\\"\\\", \\\"trimming\\\": {\\\"trimming_select\\\": \\\"\\\", \\\"__current_case__\\\": 0}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0, \\\"input_singles\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\"}", "id": 2, "tool_shed_repository": {"owner": "bgruening", "changeset_revision": "949f01671246", "name": "trim_galore", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "0533b5d9-7a59-438c-a74b-0b7687f481ea", "errors": null, "name": "Trim Galore!", "post_job_actions": {}, "label": "Trimming", "inputs": [{"name": "singlePaired", "description": "runtime parameter for tool Trim Galore!"}], "position": {"top": 831, "left": 411}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1", "type": "tool"}, "3": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_dereplication/1.9.7.0", "tool_version": "1.9.7.0", "outputs": [{"type": "fasta", "name": "outfile"}, {"type": "fasta", "name": "uc_outfile"}], "workflow_outputs": [], "input_connections": {"infile": {"output_name": "trimmed_reads_single", "id": 2}}, "tool_state": "{\"sizein\": \"\\\"false\\\"\", \"__page__\": null, \"maxuniquesize\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"minuniquesize\": \"\\\"\\\"\", \"topn\": \"\\\"\\\"\", \"strand\": \"\\\"plus\\\"\", \"infile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"sizeout\": \"\\\"false\\\"\", \"uc\": \"\\\"false\\\"\"}", "id": 3, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "576963db5f1b", "name": "vsearch", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "98dc5416-f149-4e69-874c-48c4a8a67b09", "errors": null, "name": "VSearch dereplication", "post_job_actions": {}, "label": "Dereplication", "inputs": [{"name": "infile", "description": "runtime parameter for tool VSearch dereplication"}], "position": {"top": 913, "left": 706}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/vsearch/vsearch_dereplication/1.9.7.0", "type": "tool"}, "4": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2/metaphlan2/2.6.0.0", "tool_version": "2.6.0.0", "outputs": [{"type": "tabular", "name": "output_file"}, {"type": "sam", "name": "sam_output_file"}, {"type": "biom", "name": "biom_output_file"}], "workflow_outputs": [], "input_connections": {"input_file": {"output_name": "outfile", "id": 3}}, "tool_state": "{\"min_cu_len\": \"\\\"2000\\\"\", \"min_alignment_len\": \"\\\"0\\\"\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null, \"ignore_eukaryotes\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"db\": \"{\\\"db_selector\\\": \\\"cached\\\", \\\"cached_db\\\": \\\"mpa_v20_m200\\\", \\\"__current_case__\\\": 0}\", \"stat_q\": \"\\\"0.1\\\"\", \"ignore_viruses\": \"\\\"true\\\"\", \"ignore_archaea\": \"\\\"true\\\"\", \"analysis_type\": \"{\\\"tax_lev\\\": \\\"a\\\", \\\"analysis_type_select\\\": \\\"rel_ab\\\", \\\"__current_case__\\\": 0}\", \"ignore_bacteria\": \"\\\"true\\\"\"}", "id": 4, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "8c82c4d90cc6", "name": "metaphlan2", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "7281de8c-c5df-48dd-841a-80c468b5fe75", "errors": null, "name": "MetaPhlAn2", "post_job_actions": {}, "label": "Taxonomic assignation", "inputs": [{"name": "input_file", "description": "runtime parameter for tool MetaPhlAn2"}], "position": {"top": 698, "left": 982}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2/metaphlan2/2.6.0.0", "type": "tool"}, "5": {"tool_id": "toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.5", "tool_version": "2.1b.5", "outputs": [{"type": "input", "name": "output_fastx"}, {"type": "fastq", "name": "output_paired_fastx"}, {"type": "fastq", "name": "aligned_forward"}, {"type": "fastq", "name": "aligned_reverse"}, {"type": "input", "name": "output_other"}, {"type": "fastq", "name": "output_paired_other"}, {"type": "fastq", "name": "unaligned_forward"}, {"type": "fastq", "name": "unaligned_reverse"}, {"type": "bam", "name": "output_bam"}, {"type": "tabular", "name": "output_blast"}, {"type": "txt", "name": "output_biom"}, {"type": "input", "name": "output_de_novo"}, {"type": "txt", "name": "output_log"}], "workflow_outputs": [], "input_connections": {"sequencing_type|reads": {"output_name": "outfile", "id": 3}}, "tool_state": "{\"__page__\": null, \"strand_search\": \"\\\"\\\"\", \"aligned_sam\": \"{\\\"aligned_sam_selector\\\": \\\"--sam\\\", \\\"sq\\\": \\\"false\\\", \\\"__current_case__\\\": 0}\", \"log\": \"\\\"false\\\"\", \"input_reads\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"mismatch\": \"\\\"-3\\\"\", \"sequencing_type\": \"{\\\"reads\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sequencing_type_selector\\\": \\\"not_paired\\\", \\\"__current_case__\\\": 0}\", \"ambiguous_letter\": \"\\\"-3\\\"\", \"aligned_blast\": \"{\\\"__current_case__\\\": 1, \\\"aligned_blast_selector\\\": \\\"\\\"}\", \"databases_type\": \"{\\\"databases_selector\\\": \\\"cached\\\", \\\"input_databases\\\": [\\\"2.1b-silva-bac-23s-id98\\\", \\\"2.1b-silva-bac-16s-id90\\\", \\\"2.1b-silva-euk-28s-id98\\\", \\\"2.1b-rfam-5.8s-database-id98\\\", \\\"2.1b-silva-euk-18s-id95\\\", \\\"2.1b-silva-arc-16s-id95\\\", \\\"2.1b-silva-arc-23s-id98\\\", \\\"2.1b-rfam-5s-database-id98\\\"], \\\"__current_case__\\\": 0}\", \"match\": \"\\\"2\\\"\", \"gap_open\": \"\\\"5\\\"\", \"report\": \"{\\\"report_best\\\": {\\\"report_best_min_lis\\\": \\\"2\\\", \\\"__current_case__\\\": 0, \\\"report_best_type\\\": \\\"1\\\"}, \\\"report_type\\\": \\\"best\\\", \\\"__current_case__\\\": 1, \\\"blast\\\": {\\\"blast_output\\\": \\\"False\\\", \\\"__current_case__\\\": 1}, \\\"print_all_reads\\\": \\\"false\\\", \\\"otu\\\": {\\\"otu_map\\\": \\\"False\\\", \\\"__current_case__\\\": 1}}\", \"e_value\": \"\\\"1.0\\\"\", \"aligned_fastx\": \"{\\\"aligned_fastx_selector\\\": \\\"--fastx\\\", \\\"other\\\": \\\"true\\\", \\\"__current_case__\\\": 0}\", \"gap_ext\": \"\\\"2\\\"\"}", "id": 5, "tool_shed_repository": {"owner": "rnateam", "changeset_revision": "65c38d020fea", "name": "sortmerna", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "dfaecd0c-620e-4ff0-89ca-cd1af49795c6", "errors": null, "name": "Filter with SortMeRNA", "post_job_actions": {}, "label": "rRNA/rDNA selection", "inputs": [{"name": "sequencing_type", "description": "runtime parameter for tool Filter with SortMeRNA"}], "position": {"top": 998, "left": 964.5}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/rnateam/sortmerna/bg_sortmerna/2.1b.5", "type": "tool"}, "6": {"tool_id": "toolshed.g2.bx.psu.edu/repos/bebatut/format_metaphlan2_output/format_metaphlan2_output/0.1.0", "tool_version": "0.1.0", "outputs": [{"type": "tabular", "name": "all_taxo_level_abundance_file"}, {"type": "tabular", "name": "kingdom_abundance_file"}, {"type": "tabular", "name": "phylum_abundance_file"}, {"type": "tabular", "name": "class_abundance_file"}, {"type": "tabular", "name": "order_abundance_file"}, {"type": "tabular", "name": "family_abundance_file"}, {"type": "tabular", "name": "genus_abundance_file"}, {"type": "tabular", "name": "species_abundance_file"}, {"type": "tabular", "name": "strains_abundance_file"}], "workflow_outputs": [], "input_connections": {"input_file": {"output_name": "output_file", "id": 4}}, "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", "id": 6, "tool_shed_repository": {"owner": "bebatut", "changeset_revision": "2bfa9b200600", "name": "format_metaphlan2_output", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "be78f650-b4ec-4373-8e3a-d677aaed5e22", "errors": null, "name": "Format MetaPhlAn2", "post_job_actions": {}, "label": "Formatting for the different taxonomic levels", "inputs": [{"name": "input_file", "description": "runtime parameter for tool Format MetaPhlAn2"}], "position": {"top": 100, "left": 1263}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bebatut/format_metaphlan2_output/format_metaphlan2_output/0.1.0", "type": "tool"}, "7": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2krona/metaphlan2krona/2.6.0.0", "tool_version": "2.6.0.0", "outputs": [{"type": "tabular", "name": "krona"}], "workflow_outputs": [], "input_connections": {"profile": {"output_name": "output_file", "id": 4}}, "tool_state": "{\"profile\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", "id": 7, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "fdbd63e92b01", "name": "metaphlan2krona", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "5993071a-004b-4a52-8499-5705a6c26742", "errors": null, "name": "Format MetaPhlAn2", "post_job_actions": {}, "label": null, "inputs": [{"name": "profile", "description": "runtime parameter for tool Format MetaPhlAn2"}], "position": {"top": 431, "left": 1331}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/metaphlan2krona/metaphlan2krona/2.6.0.0", "type": "tool"}, "8": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.19", "tool_version": "0.19", "outputs": [{"type": "txt", "name": "tree"}, {"type": "txt", "name": "annotation"}], "workflow_outputs": [], "input_connections": {"lefse_input": {"output_name": "output_file", "id": 4}}, "tool_state": "{\"ftop\": \"\\\"\\\"\", \"background_clades\": \"\\\"\\\"\", \"max_clade_size\": \"\\\"200\\\"\", \"def_font_size\": \"\\\"10\\\"\", \"external_annotations\": \"\\\"\\\"\", \"annotation_legend_font_size\": \"\\\"10\\\"\", \"__page__\": null, \"skip_rows\": \"\\\"\\\"\", \"title\": \"\\\"\\\"\", \"__rerun_remap_job_id__\": null, \"metadata_rows\": \"\\\"\\\"\", \"least_biomarkers\": \"\\\"\\\"\", \"min_clade_size\": \"\\\"20\\\"\", \"sperc\": \"\\\"\\\"\", \"fperc\": \"\\\"\\\"\", \"annotations\": \"\\\"\\\"\", \"lefse_input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"background_colors\": \"\\\"\\\"\", \"def_clade_size\": \"\\\"10\\\"\", \"stop\": \"\\\"\\\"\", \"sname_row\": \"\\\"0\\\"\", \"max_font_size\": \"\\\"12\\\"\", \"fname_row\": \"\\\"0\\\"\", \"abundance_threshold\": \"\\\"20.0\\\"\", \"title_font_size\": \"\\\"15\\\"\", \"input_lefse_output\": \"{\\\"input_lefse_output_test\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\", \"background_levels\": \"\\\"\\\"\", \"min_font_size\": \"\\\"8\\\"\", \"most_abundant\": \"\\\"\\\"\"}", "id": 8, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "ed1becc01910", "name": "export2graphlan", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "2b184419-ebe1-40d0-b404-9048e3cfd20c", "errors": null, "name": "Export to GraPhlAn", "post_job_actions": {}, "label": null, "inputs": [{"name": "lefse_input", "description": "runtime parameter for tool Export to GraPhlAn"}], "position": {"top": 545, "left": 1326}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/export2graphlan/export2graphlan/0.19", "type": "tool"}, "9": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/humann2/humann2/0.11.1.0", "tool_version": "0.11.1.0", "outputs": [{"type": "tsv", "name": "gene_families_tsv"}, {"type": "biom1", "name": "gene_families_biom"}, {"type": "tsv", "name": "pathcoverage_tsv"}, {"type": "biom1", "name": "pathcoverage_biom"}, {"type": "tsv", "name": "pathabundance_tsv"}, {"type": "biom1", "name": "pathabundance_biom"}], "workflow_outputs": [], "input_connections": {"input": {"output_name": "output_other", "id": 5}, "taxo_profile|taxonomic_profile": {"output_name": "output_file", "id": 4}}, "tool_state": "{\"adv\": \"{\\\"translated_query_coverage_threshold\\\": \\\"50.0\\\", \\\"translated_subject_coverage_threshold\\\": \\\"50.0\\\", \\\"prescreen_threshold\\\": \\\"0.01\\\", \\\"evalue\\\": \\\"1.0\\\", \\\"annotation_gene_index\\\": \\\"8\\\", \\\"minpath\\\": \\\"true\\\", \\\"id_mapping\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"identity_threshold\\\": \\\"50.0\\\", \\\"remove_statified_output\\\": \\\"false\\\", \\\"xipe\\\": \\\"false\\\", \\\"pick_frames\\\": \\\"true\\\", \\\"gap_fill\\\": \\\"true\\\", \\\"output_format\\\": \\\"tsv\\\", \\\"remove_column_description_output\\\": \\\"false\\\", \\\"output_max_dec\\\": \\\"10\\\"}\", \"__page__\": null, \"bypass\": \"{\\\"bypass_translated_search\\\": \\\"false\\\", \\\"bypass_nucleotide_search\\\": \\\"false\\\", \\\"bypass_prescreen\\\": \\\"false\\\", \\\"bypass_nucleotide_index\\\": \\\"false\\\"}\", \"translated_alignment\": \"\\\"diamond\\\"\", \"__rerun_remap_job_id__\": null, \"taxo_profile\": \"{\\\"taxonomic_profile_test\\\": \\\"true\\\", \\\"taxonomic_profile\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"pathways\": \"\\\"metacyc\\\"\", \"nucleotide_db\": \"{\\\"nucleotide_db_selector\\\": \\\"cached\\\", \\\"nucleotide_database\\\": \\\"chocophlan-full-2018-01-22\\\", \\\"__current_case__\\\": 0}\", \"search_mode\": \"\\\"uniref50\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"protein_db\": \"{\\\"protein_db_selector\\\": \\\"cached\\\", \\\"__current_case__\\\": 0, \\\"protein_database\\\": \\\"uniref-uniref50_diamond-2018-01-22\\\"}\"}", "id": 9, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "ca82f52681af", "name": "humann2", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "51a8b591-8fe0-43f7-ad38-0d2ea2c217d6", "errors": null, "name": "HUMAnN2", "post_job_actions": {}, "label": "Metabolic assignation", "inputs": [{"name": "adv", "description": "runtime parameter for tool HUMAnN2"}, {"name": "taxo_profile", "description": "runtime parameter for tool HUMAnN2"}, {"name": "input", "description": "runtime parameter for tool HUMAnN2"}], "position": {"top": 918, "left": 1237}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/humann2/humann2/0.11.1.0", "type": "tool"}, "10": {"tool_id": "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1", "tool_version": "2.6.1", "outputs": [{"type": "html", "name": "output"}], "workflow_outputs": [], "input_connections": {"type_of_data|input": {"output_name": "krona", "id": 7}}, "tool_state": "{\"__page__\": null, \"__rerun_remap_job_id__\": null, \"combine_inputs\": \"\\\"false\\\"\", \"type_of_data\": \"{\\\"input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"type_of_data_selector\\\": \\\"text\\\", \\\"__current_case__\\\": 1}\", \"root_name\": \"\\\"Root\\\"\"}", "id": 10, "tool_shed_repository": {"owner": "crs4", "changeset_revision": "d41b98e72c4c", "name": "taxonomy_krona_chart", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "705bc931-908a-459d-8d8a-5c6b14286151", "errors": null, "name": "Krona pie chart", "post_job_actions": {}, "label": "Visualisation (KRONA)", "inputs": [{"name": "type_of_data", "description": "runtime parameter for tool Krona pie chart"}], "position": {"top": 406, "left": 1606}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.6.1", "type": "tool"}, "11": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.0.0.0", "tool_version": "1.0.0.0", "outputs": [{"type": "phyloxml", "name": "output_tree"}], "workflow_outputs": [], "input_connections": {"input_tree": {"output_name": "tree", "id": 8}, "annot": {"output_name": "annotation", "id": 8}}, "tool_state": "{\"input_tree\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"annot\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__page__\": null}", "id": 11, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "5d6f8f0bef7c", "name": "graphlan_annotate", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "17c154d8-fbb8-4745-a5f6-62a5b653d0bf", "errors": null, "name": "Generation, personalization and annotation of tree", "post_job_actions": {}, "label": null, "inputs": [{"name": "input_tree", "description": "runtime parameter for tool Generation, personalization and annotation of tree"}, {"name": "annot", "description": "runtime parameter for tool Generation, personalization and annotation of tree"}], "position": {"top": 539, "left": 1582}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/graphlan_annotate/graphlan_annotate/1.0.0.0", "type": "tool"}, "12": {"tool_id": "toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.1.0", "tool_version": "0.1.0", "outputs": [{"type": "tabular", "name": "gene_families_output_file"}, {"type": "tabular", "name": "pathway_output_file"}], "workflow_outputs": [], "input_connections": {"metaphlan2_file": {"output_name": "output_file", "id": 4}, "humann2_file": {"output_name": "gene_families_tsv", "id": 9}}, "tool_state": "{\"metaphlan2_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"humann2_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"type\": \"\\\"gene_families\\\"\", \"__page__\": null}", "id": 12, "tool_shed_repository": {"owner": "bebatut", "changeset_revision": "31394a0c0242", "name": "combine_metaphlan2_humann2", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "ee12a2ef-1d55-43f1-b0a2-cbe005539b0d", "errors": null, "name": "Combine MetaPhlAn2 and HUMAnN2 outputs", "post_job_actions": {}, "label": "Combination of taxonomic and metabolic assignations for gene families", "inputs": [{"name": "metaphlan2_file", "description": "runtime parameter for tool Combine MetaPhlAn2 and HUMAnN2 outputs"}, {"name": "humann2_file", "description": "runtime parameter for tool Combine MetaPhlAn2 and HUMAnN2 outputs"}], "position": {"top": 686, "left": 1560.5}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.1.0", "type": "tool"}, "13": {"tool_id": "toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.1.0", "tool_version": "0.1.0", "outputs": [{"type": "tabular", "name": "gene_families_output_file"}, {"type": "tabular", "name": "pathway_output_file"}], "workflow_outputs": [], "input_connections": {"metaphlan2_file": {"output_name": "output_file", "id": 4}, "humann2_file": {"output_name": "pathabundance_tsv", "id": 9}}, "tool_state": "{\"metaphlan2_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"humann2_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"type\": \"\\\"gene_families\\\"\", \"__page__\": null}", "id": 13, "tool_shed_repository": {"owner": "bebatut", "changeset_revision": "31394a0c0242", "name": "combine_metaphlan2_humann2", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "5d19d8f9-2e6c-4506-a62a-636c242277a9", "errors": null, "name": "Combine MetaPhlAn2 and HUMAnN2 outputs", "post_job_actions": {}, "label": "Combination of taxonomic and metabolic assignations for pathways", "inputs": [{"name": "metaphlan2_file", "description": "runtime parameter for tool Combine MetaPhlAn2 and HUMAnN2 outputs"}, {"name": "humann2_file", "description": "runtime parameter for tool Combine MetaPhlAn2 and HUMAnN2 outputs"}], "position": {"top": 1137, "left": 1640.5}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bebatut/combine_metaphlan2_humann2/combine_metaphlan2_humann2/0.1.0", "type": "tool"}, "14": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/humann2_genefamilies_genus_level/humann2_genefamilies_genus_level/0.11.1.0", "tool_version": "0.11.1.0", "outputs": [{"type": "tsv", "name": "output"}], "workflow_outputs": [], "input_connections": {"input": {"output_name": "gene_families_tsv", "id": 9}}, "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}", "id": 14, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "5628423eb63e", "name": "humann2_genefamilies_genus_level", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "5a93decf-fca2-419e-a979-c5ab7d51d362", "errors": null, "name": "Create a genus level gene families file", "post_job_actions": {}, "label": null, "inputs": [{"name": "input", "description": "runtime parameter for tool Create a genus level gene families file"}], "position": {"top": 785, "left": 1866.5}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/humann2_genefamilies_genus_level/humann2_genefamilies_genus_level/0.11.1.0", "type": "tool"}, "15": {"tool_id": "toolshed.g2.bx.psu.edu/repos/bebatut/group_humann2_uniref_abundances_to_go/group_humann2_uniref_abundances_to_go/1.2.0", "tool_version": "1.2.0", "outputs": [{"type": "tabular", "name": "molecular_function_abundance"}, {"type": "tabular", "name": "biological_process_abundance"}, {"type": "tabular", "name": "cellular_component_abundance"}], "workflow_outputs": [], "input_connections": {"humann2_gene_families_abundance": {"output_name": "gene_families_tsv", "id": 9}}, "tool_state": "{\"__page__\": null, \"gene_ontology\": \"{\\\"gene_ontology_test\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\", \"slim_gene_ontology\": \"{\\\"slim_gene_ontology_test\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\", \"humann2_gene_families_abundance\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"uniref50_go\": \"{\\\"uniref50_go_test\\\": \\\"false\\\", \\\"__current_case__\\\": 1}\"}", "id": 15, "tool_shed_repository": {"owner": "bebatut", "changeset_revision": "cad28d7b49d2", "name": "group_humann2_uniref_abundances_to_go", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "c5c483ec-a212-4742-9da3-544ad53108b7", "errors": null, "name": "Group abundances", "post_job_actions": {}, "label": "Grouping to high level GO Slim terms", "inputs": [{"name": "humann2_gene_families_abundance", "description": "runtime parameter for tool Group abundances"}], "position": {"top": 906, "left": 1868}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/bebatut/group_humann2_uniref_abundances_to_go/group_humann2_uniref_abundances_to_go/1.2.0", "type": "tool"}, "16": {"tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.0.0.0", "tool_version": "1.0.0.0", "outputs": [{"type": "png", "name": "png_output_image"}, {"type": "pdf", "name": "pdf_output_image"}, {"type": "ps", "name": "ps_output_image"}, {"type": "eps", "name": "eps_output_image"}, {"type": "svg", "name": "svg_output_image"}], "workflow_outputs": [], "input_connections": {"input_tree": {"output_name": "output_tree", "id": 11}}, "tool_state": "{\"__page__\": null, \"input_tree\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"pad\": \"\\\"\\\"\", \"image_format\": \"{\\\"dpi\\\": \\\"\\\", \\\"__current_case__\\\": 0, \\\"format\\\": \\\"png\\\"}\", \"size\": \"\\\"7\\\"\"}", "id": 16, "tool_shed_repository": {"owner": "iuc", "changeset_revision": "8f62f666dcb6", "name": "graphlan", "tool_shed": "toolshed.g2.bx.psu.edu"}, "uuid": "324857c9-bfd9-4fcb-8183-f7dcab4651a3", "errors": null, "name": "GraPhlAn", "post_job_actions": {}, "label": "Visualisation (GraPhlAn)", "inputs": [{"name": "input_tree", "description": "runtime parameter for tool GraPhlAn"}], "position": {"top": 510, "left": 1928}, "annotation": "", "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/graphlan/graphlan/1.0.0.0", "type": "tool"}}, "annotation": "", "a_galaxy_workflow": "true"}, "workflow_outputs": [], "input_connections": {"Raw reads": {"input_subworkflow_step_id": 0, "output_name": "output", "id": 0}}, "id": 1, "uuid": "5d02d481-1110-4fab-bb1d-e7c386b7f98f", "name": "Shotgun workflow", "label": null, "position": {"top": 324, "left": 506}, "annotation": "", "type": "subworkflow"}}, "annotation": "", "a_galaxy_workflow": "true"} \ No newline at end of file