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fixing spaces in param descriptions
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@Sann5
Sann5 committed Oct 9, 2023
1 parent 8a92a5e commit 529d7dd
Showing 1 changed file with 24 additions and 24 deletions.
48 changes: 24 additions & 24 deletions q2_moshpit/plugin_setup.py
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kraken2_param_descriptions = {
"threads": "Number of threads.",
"confidence": "Confidence score threshold.",
"minimum_base_quality": "Minimum base quality used in classification."
" Only applies when reads are used as input.",
"minimum_base_quality": "Minimum base quality used in classification. "
"Only applies when reads are used as input.",
"memory_mapping": "Avoids loading the database into RAM.",
"minimum_hit_groups": "Minimum number of hit groups (overlapping "
"k-mers sharing the same minimizer).",
"quick": "Quick operation (use first hit or hits).",
"report_minimizer_data": "Include number of read-minimizers per-taxon and"
" unique read-minimizers per-taxon in the repot.",
"report_minimizer_data": "Include number of read-minimizers per-taxon and "
"unique read-minimizers per-taxon in the repot.",
}

plugin = Plugin(
Expand Down Expand Up @@ -125,7 +125,7 @@
output_descriptions={
"mags": "The resulting MAGs.",
"contig_map": "Mapping of MAG identifiers to the contig identifiers "
"contained in each MAG.",
"contained in each MAG.",
"unbinned_contigs": "Contigs that were not binned into any MAG.",
},
name="Bin contigs into MAGs using MetaBAT 2.",
Expand Down Expand Up @@ -173,7 +173,7 @@
},
name="Perform taxonomic classification of reads or MAGs using Kraken 2.",
description="This method uses Kraken 2 to classify provided NGS reads "
"or MAGs into taxonomic groups.",
"or MAGs into taxonomic groups.",
citations=[citations["wood2019"]],
)

Expand Down Expand Up @@ -282,8 +282,8 @@
},
name="Build Kraken 2 database.",
description="This method builds a Kraken 2/Bracken databases from "
"provided DNA sequences or simply fetches pre-built "
"versions from an online resource.",
"provided DNA sequences or simply fetches pre-built "
"versions from an online resource.",
citations=[citations["wood2019"], citations["lu2017"]],
)

Expand Down Expand Up @@ -332,13 +332,13 @@
],
input_descriptions={"reports": "Per-sample Kraken 2 reports."},
parameter_descriptions={
"coverage_threshold": "The minimum percent coverage required to"
" produce a feature."
"coverage_threshold": "The minimum percent coverage required to "
"produce a feature."
},
output_descriptions={
"table": "A presence/absence table of selected features. The features"
" are not of even ranks, but will be the most specific rank"
" available.",
"table": "A presence/absence table of selected features. The features "
"are not of even ranks, but will be the most specific rank "
"available.",
"taxonomy": "Infra-clade ranks are ignored "
"unless they are strain-level. Missing internal ranks "
"are annotated by their next most specific rank, "
Expand All @@ -347,8 +347,8 @@
},
name="Select downstream features from Kraken 2",
description="Convert a Kraken 2 report, which is an annotated NCBI "
"taxonomy tree into generic artifacts for downstream "
"analyses.",
"taxonomy tree into generic artifacts for downstream "
"analyses.",
)

plugin.methods.register_function(
Expand All @@ -373,7 +373,7 @@
# 'taxonomic assignments of its contigs. '
},
output_descriptions={
'taxonomy': 'Infra-clade ranks are ignored'
'taxonomy': 'Infra-clade ranks are ignored '
'unless they are strain-level. Missing internal ranks '
'are annotated by their next most specific rank, '
'with the exception of k__Bacteria and k__Archaea which '
Expand All @@ -398,7 +398,7 @@
input_descriptions={
'sequences': 'Sequence data of the contigs we want to '
'search for hits using the Diamond Database',
'diamond_db': 'The filepath to an artifact containing the'
'diamond_db': 'The filepath to an artifact containing the '
'Diamond database',
},
parameter_descriptions={
Expand Down Expand Up @@ -475,8 +475,8 @@
busco_param_descriptions = {
"mode": "Specify which BUSCO analysis mode to run."
"Currently only the 'genome' or 'geno' option is supported, "
"for genome assemblies. In the future modes for transcriptome"
"assemblies and for annotated gene sets (proteins) will be made"
"for genome assemblies. In the future modes for transcriptome "
"assemblies and for annotated gene sets (proteins) will be made "
"available.",
"lineage_dataset": "Specify the name of the BUSCO lineage to be used. "
"To see all possible options run `busco "
Expand All @@ -489,7 +489,7 @@
"Example: '--PARAM1=VALUE1,--PARAM2=VALUE2'.",
"augustus_species": "Specify a species for Augustus training.",
"auto_lineage": "Run auto-lineage to find optimum lineage path.",
"auto_lineage_euk": "Run auto-placement just on eukaryote tree to find"
"auto_lineage_euk": "Run auto-placement just on eukaryote tree to find "
"optimum lineage path.",
"auto_lineage_prok": "Run auto-lineage just on non-eukaryote trees to "
"find optimum lineage path.",
Expand Down Expand Up @@ -521,11 +521,11 @@
"metaeuk_parameters": "Pass additional arguments to Metaeuk for the first "
"run. All arguments should be contained within a "
"single string with no white space, with each "
"argument separated by a comma."
"argument separated by a comma. "
"Example: `--PARAM1=VALUE1,--PARAM2=VALUE2`.",
"metaeuk_rerun_parameters": "Pass additional arguments to Metaeuk for the "
"second run. All arguments should be "
"contained within a single string with no"
"contained within a single string with no "
"white space, with each argument separated by "
"a comma. "
"Example: `--PARAM1=VALUE1,--PARAM2=VALUE2`.",
Expand Down Expand Up @@ -555,8 +555,8 @@
parameter_descriptions=busco_param_descriptions,
name="Evaluate quality of the generated MAGs using BUSCO.",
description="This method uses BUSCO "
"(Benchmarking Universal Single-Copy Ortholog assessment tool)"
" to assess the quality of assembled MAGs and generates "
"(Benchmarking Universal Single-Copy Ortholog assessment "
"tool) to assess the quality of assembled MAGs and generates "
"visualizations summarizing the results.",
citations=[citations["manni_busco_2021"]],
)

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