ebi-gene-expression-group · nomadscientist · Nov 5, 2024 · Nov 5, 2024 · Nov 5, 2024 · Nov 5, 2024
diff --git a/tools/tertiary-analysis/cell-types-analysis/ct_build_cell_ontology_dict.xml b/tools/tertiary-analysis/cell-types-analysis/ct_build_cell_ontology_dict.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>ct_macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         mkdir -p input_dir;
@@ -12,7 +13,7 @@
 
         build_cell_ontology_dict.R --input-dir input_dir  --output-dict-path "${output_dict_path}" --output-text-path "${output_txt_path}"
         #if $condensed_sdrf
-        --condensed-sdrf "${condensed_sdrf}" 
+        --condensed-sdrf "${condensed_sdrf}"
         #end if
         #if $barcode_col_name
         --barcode-col-name "${barcode_col_name}"
@@ -21,7 +22,7 @@
         --cell-label-col-name "${cell_label_col_name}"
         #end if
         #if $cell_ontology_col_name
-        --cell-ontology-col-name "${cell_ontology_col_name}" 
+        --cell-ontology-col-name "${cell_ontology_col_name}"
         #end if
          ]]></command>
     <inputs>
@@ -50,7 +51,7 @@
     </tests>
     <help><![CDATA[
     @HELP@
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />

diff --git a/tools/tertiary-analysis/cell-types-analysis/ct_check_labels.xml b/tools/tertiary-analysis/cell-types-analysis/ct_check_labels.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>ct_macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
 
@@ -14,15 +15,15 @@
 
         ]]></command>
         <inputs>
-            
+
             <param type="data" name="input_file" label="Input File" multiple="true" format="txt" help="Input metadta file" />
             <param type="text" name="label_field" label="Label Field" optional="true" help="Name of label field in metadata file">
                 <expand macro="sanitize_strings" />
             </param>
-            <param type="boolean" name="condensed" checked="false" label="Condensed Metadata File" help="Are the supplied metadata files of condensed format?" /> 
+            <param type="boolean" name="condensed" checked="false" label="Condensed Metadata File" help="Are the supplied metadata files of condensed format?" />
             <param type="integer" name="attribute_type_col_num" value='5' label="Number of Attribute Type Column" help="Number of the attribute type field in condensed metadata file. Default: 5" />
             <param type="integer" name="variable_col_num" value='6' label="Number of Label Column" help="Number of the label field in condensed metadata file. Default: 6" />
-            <param type="boolean" name="avoid_lowercase" checked="false" label="Avoid Lowercaase" help="Should setting the labels to lowercase be skipped? Default: False" /> 
+            <param type="boolean" name="avoid_lowercase" checked="false" label="Avoid Lowercaase" help="Should setting the labels to lowercase be skipped? Default: False" />
 
         </inputs>
         <outputs>
@@ -38,7 +39,7 @@
     </tests>
         <help><![CDATA[
     @HELP@
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />

diff --git a/tools/tertiary-analysis/cell-types-analysis/ct_combine_tool_outputs.xml b/tools/tertiary-analysis/cell-types-analysis/ct_combine_tool_outputs.xml
@@ -3,14 +3,15 @@
     <macros>
         <import>ct_macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         mkdir -p input_dir;
         #for $table in $input_tables:
           cp '$table' input_dir/;
         #end for
 
-        combine_tool_outputs.R --input-dir input_dir --top-labels-num "${top_labels_num}" --scores "${scores}" --output-table "${output_table}" 
+        combine_tool_outputs.R --input-dir input_dir --top-labels-num "${top_labels_num}" --scores "${scores}" --output-table "${output_table}"
 
         #if $exclusions
         --exclusions "${exclusions}"
@@ -35,7 +36,7 @@
     </tests>
     <help><![CDATA[
     @HELP@
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />

diff --git a/tools/tertiary-analysis/cell-types-analysis/ct_downsample_cells.xml b/tools/tertiary-analysis/cell-types-analysis/ct_downsample_cells.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>ct_macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         ln -s "${matrix}" matrix.mtx &&
@@ -53,7 +54,7 @@
 
     <help><![CDATA[
     @HELP@
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />

diff --git a/tools/tertiary-analysis/cell-types-analysis/ct_get_consensus_outputs.xml b/tools/tertiary-analysis/cell-types-analysis/ct_get_consensus_outputs.xml
@@ -3,13 +3,14 @@
     <macros>
         <import>ct_macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         mkdir -p input_dir;
         #for $table in $input_tables:
           cp '$table' input_dir/;
         #end for
-        
+
         get_consensus_output.R --input-dir input_dir --parallel "TRUE" --num-cores \${GALAXY_SLOTS:-1} --cl-dictionary "${lab_cl_mapping}"   --summary-table-output-path "${summary_table_output_path}" --raw-table-output-path "${raw_table_output_path}" --tmpdir ./
         #if $tool_table
         --tool-table "${tool_table}"
@@ -27,10 +28,10 @@
         --exclusions "${exclusions}"
         #end if
         #if $sem_siml_metric
-        --semantic-sim-metric "${sem_siml_metric}" 
+        --semantic-sim-metric "${sem_siml_metric}"
         #end if
         #if $true_labels
-        --true-labels "${true_labels}" 
+        --true-labels "${true_labels}"
         #end if
          ]]></command>
     <inputs>
@@ -60,7 +61,7 @@
     </tests>
     <help><![CDATA[
     @HELP@
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />

diff --git a/tools/tertiary-analysis/cell-types-analysis/ct_get_empirical_dist.xml b/tools/tertiary-analysis/cell-types-analysis/ct_get_empirical_dist.xml
@@ -3,14 +3,15 @@
     <macros>
         <import>ct_macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
 
-        get_empirical_dist.R --input-ref-file "${input_ref_file}" --label-column-ref "${label_col_ref}" --lab-cl-mapping "${lab_cl_mapping}" --num-iterations "${num_iter}"  --parallel "TRUE" --num-cores \${GALAXY_SLOTS:-1} --tmpdir ./  --output-path "${output_list_path}" 
+        get_empirical_dist.R --input-ref-file "${input_ref_file}" --label-column-ref "${label_col_ref}" --lab-cl-mapping "${lab_cl_mapping}" --num-iterations "${num_iter}"  --parallel "TRUE" --num-cores \${GALAXY_SLOTS:-1} --tmpdir ./  --output-path "${output_list_path}"
 
         #if $ontology_graph
         --ontology-graph "${ontology_graph}"
-        #end if 
+        #end if
         #if $sample_labs
         --sample-labs "${sample_labs}"
         #end if

diff --git a/tools/tertiary-analysis/cell-types-analysis/ct_get_tool_perf_table.xml b/tools/tertiary-analysis/cell-types-analysis/ct_get_tool_perf_table.xml
@@ -3,14 +3,15 @@
     <macros>
          <import>ct_macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         mkdir -p input_dir;
         #for $input_file in $input_files:
           cp '$input_file' input_dir/;
         #end for
 
-        get_tool_performance_table.R --input-dir input_dir --ref-file "${ref_file}" --parallel "TRUE" --num-cores \${GALAXY_SLOTS:-1} --lab-cl-mapping "${lab_cl_mapping}" --output-path "${output_path}" --tmpdir ./  
+        get_tool_performance_table.R --input-dir input_dir --ref-file "${ref_file}" --parallel "TRUE" --num-cores \${GALAXY_SLOTS:-1} --lab-cl-mapping "${lab_cl_mapping}" --output-path "${output_path}" --tmpdir ./
 
         #if $exclusions
         --exclusions "${exclusions}"
@@ -28,13 +29,13 @@
         --barcode-col-pred "${barcode_col_pred}"
         #end if
         #if $label_col_ref
-        --label-column-ref "${label_col_ref}" 
+        --label-column-ref "${label_col_ref}"
         #end if
         #if $label_col_pred
-        --label-column-pred "${label_col_pred}" 
+        --label-column-pred "${label_col_pred}"
         #end if
         #if $sem_siml_metric
-        --semantic-sim-metric "${sem_siml_metric}" 
+        --semantic-sim-metric "${sem_siml_metric}"
         #end if
 
          ]]></command>
@@ -77,8 +78,8 @@
     </tests>
     <help><![CDATA[
     @HELP@
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />
-</tool> 
+</tool>
diff --git a/tools/tertiary-analysis/cell-types-analysis/ct_get_tool_pvals.xml b/tools/tertiary-analysis/cell-types-analysis/ct_get_tool_pvals.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>ct_macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         get_tool_pvals.R --input-table "${input_table}" --emp-dist-list "${emp_dist_list}" --output-table "${output_table}" ]]></command>
@@ -22,7 +23,7 @@
     </tests>
     <help><![CDATA[
     @HELP@
-    
+
     @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />

diff --git a/tools/tertiary-analysis/cell-types-analysis/ct_macros.xml b/tools/tertiary-analysis/cell-types-analysis/ct_macros.xml
@@ -2,6 +2,11 @@
     <token name="@TOOL_VERSION@">1.1.1</token>
     <token name="@HELP@">More information can be found at https://github.com/ebi-gene-expression-group/cell-types-analysis</token>
     <token name="@PROFILE@">18.01</token>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">cell_types_analysis</xref>
+        </xrefs>
+    </xml>
     <xml name="requirements">
       <requirements>
         <requirement type="package" version="0.1.9">cell-types-analysis</requirement>
@@ -17,7 +22,7 @@
 **Version history**
 0.1.6+galaxy0: Add removing non-alphanumeric characters from labels in metadata files
 0.0.5+galaxy0: Initial contribution. Andrey Solovyev, Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/.
-0.0.5+galaxy1: Standardise input/output format into .txt. 
+0.0.5+galaxy1: Standardise input/output format into .txt.
     ]]></token>
     <xml name="sem_siml_options">
       <param type="select" name="sem_siml_metric" label="Semantic similarity metric"  help="What semantic similarity metric should be used? NB: if include-sem-siml is set to True, make sure to use a metric that is in the [0;1] interval. See https://www.bioconductor.org/packages/release/bioc/html/Onassis.html for more detail.">

diff --git a/tools/tertiary-analysis/data-hca/matrix-service.xml b/tools/tertiary-analysis/data-hca/matrix-service.xml
@@ -1,6 +1,9 @@
 <?xml version="1.0" encoding="utf-8"?>
 <tool id="hca_matrix_downloader" name="Human Cell Atlas Matrix Downloader" version="v0.0.4+galaxy0">
   <description>retrieves expression matrices and metadata from the Human Cell Atlas.</description>
+  <xrefs>
+      <xref type="bio.tools">human_cell_atlas_matrix_downloader</xref>
+  </xrefs>
   <requirements>
     <requirement type="package" version="0.0.4">hca-matrix-downloader</requirement>
   </requirements>

diff --git a/tools/tertiary-analysis/data-scxa/retrieve-scxa.xml b/tools/tertiary-analysis/data-scxa/retrieve-scxa.xml
@@ -1,6 +1,9 @@
 <?xml version="1.0" encoding="utf-8"?>
 <tool id="retrieve_scxa" name="EBI SCXA Data Retrieval" version="v0.0.2+galaxy2">
   <description>Retrieves expression matrixes and metadata from EBI Single Cell Expression Atlas (SCXA)</description>
+  <xrefs>
+      <xref type="bio.tools">ebi_scxa_data_retrieval</xref>
+  </xrefs>
   <requirements>
     <requirement type="package" version="1.20.1">wget</requirement>
   </requirements>

diff --git a/tools/tertiary-analysis/decoupler/decoupler_aucell_score.xml b/tools/tertiary-analysis/decoupler/decoupler_aucell_score.xml
@@ -3,6 +3,9 @@
     <description>
         scores cells using the AUCell method for gene sets.
     </description>
+    <xrefs>
+      <xref type="bio.tools">decoupler</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="1.4.0">decoupler</requirement>
     </requirements>
@@ -173,4 +176,4 @@ If the "write_anndata" parameter is set to "true", the tool will write the modif
     <citations>
         <citation type="doi">10.1093/bioadv/vbac016</citation>
     </citations>
-</tool>
+</tool>
diff --git a/tools/tertiary-analysis/decoupler/decoupler_pathway_inference.xml b/tools/tertiary-analysis/decoupler/decoupler_pathway_inference.xml
@@ -2,6 +2,9 @@
     <description>
         of functional genesets/pathways for scRNA-seq data.
     </description>
+    <xrefs>
+      <xref type="bio.tools">decoupler</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="1.4.0">decoupler</requirement>
     </requirements>
@@ -121,7 +124,7 @@ Usage
 
 This tool extracts pathway activity inference using decoupler.
 
-**Input** 
+**Input**
 
 The input file should be an AnnData object in H5AD format. The tool accepts an H5AD file containing raw or normalized data.
 
@@ -143,7 +146,7 @@ You can also specify whether to use the raw data in the AnnData object instead o
 
 The tool outputs an AnnData object containing the scores in the "obs" field, and tab-separated text files containing the scores for each cell.
 
-If the "write_activities_path" parameter is set to "true", the tool will write the modified AnnData object to an H5AD file. 
+If the "write_activities_path" parameter is set to "true", the tool will write the modified AnnData object to an H5AD file.
 If the "write_inference" parameter is set to "true", the tool will output a tab-separated text file containing the scores for each cell.
 
 

diff --git a/tools/tertiary-analysis/decoupler/decoupler_pseudobulk.xml b/tools/tertiary-analysis/decoupler/decoupler_pseudobulk.xml
@@ -1,5 +1,8 @@
 <tool id="decoupler_pseudobulk" name="Decoupler pseudo-bulk" version="1.4.0+galaxy8" profile="20.05">
     <description>aggregates single cell RNA-seq data for running bulk RNA-seq methods</description>
+    <xrefs>
+      <xref type="bio.tools">decoupler</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="1.4.0">decoupler</requirement>
     </requirements>

diff --git a/tools/tertiary-analysis/garnett/garnett_check_markers.xml b/tools/tertiary-analysis/garnett/garnett_check_markers.xml
@@ -3,29 +3,30 @@
     <macros>
         <import>garnett_macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         garnett_check_markers.R --cds-object '${cds_object}' --marker-file-path '${marker_file_path}' --database '${database}' --marker-output-path '${marker_output_path}'
 
         #if $cds_gene_id_type
-        --cds-gene-id-type '${cds_gene_id_type}' 
+        --cds-gene-id-type '${cds_gene_id_type}'
         #end if
         #if $marker_file_gene_id_type
         --marker-file-gene-id-type '${marker_file_gene_id_type}'
         #end if
         #if $plot_output_path
-        --plot-output-path '${plot_output_path}' 
+        --plot-output-path '${plot_output_path}'
         #end if
         #if $propogate_markers
-        --propogate-markers '${propogate_markers}'  
+        --propogate-markers '${propogate_markers}'
         #end if
         #if $propogate_markers
         --classifier-gene-id-type '${classifier_gene_id_type}'
         #end if
     ]]></command>
     <inputs>
         <param type="data" name="cds_object" label="CDS object" format="rdata" help="CDS object with expression data for training" />
-        <param type="data" name="marker_file_path" format="txt" label="Marker file path" help="File with marker genes specifying cell types. 
+        <param type="data" name="marker_file_path" format="txt" label="Marker file path" help="File with marker genes specifying cell types.
         See https://cole-trapnell-lab.github.io/garnett/docs/#constructing-a-marker-file for specification of the file format" />
         <param type="text" name="database" label="gene database" value="org.Hs.eg.db" help="argument for Bioconductor AnnotationDb-class package used for converting gene IDs" />
         <param type="text" name="cds_gene_id_type" label="CDS gene id type" value="ENSEMBL" help="Format of the gene IDs in your CDS object" />
@@ -52,4 +53,3 @@
     ]]></help>
      <expand macro="citations" />
 </tool>
-
diff --git a/tools/tertiary-analysis/garnett/garnett_classify_cells.xml b/tools/tertiary-analysis/garnett/garnett_classify_cells.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>garnett_macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         garnett_classify_cells.R --cds-object '${cds_object}' --classifier-object '${classifier_object}' --database '${database}' --cds-output-obj '${cds_output_obj}'
@@ -42,4 +43,3 @@
     ]]></help>
      <expand macro="citations" />
 </tool>
-
diff --git a/tools/tertiary-analysis/garnett/garnett_get_feature_genes.xml b/tools/tertiary-analysis/garnett/garnett_get_feature_genes.xml
@@ -3,6 +3,7 @@
     <macros>
         <import>garnett_macros.xml</import>
     </macros>
+    <expand macro="xrefs"/>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
         garnett_get_feature_genes.R --classifier-object '${classifier_object}'  --database '${database}' --output-path '${output_path}'
@@ -29,4 +30,4 @@
         @VERSION_HISTORY@
     ]]></help>
      <expand macro="citations" />
-</tool>
+</tool>