Add bio.tools entries to tools

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>

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.
 
 

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>

tools/tertiary-analysis/garnett/garnett_check_markers.xml

@@ -4,28 +4,29 @@
         <import>garnett_macros.xml</import>
     </macros>
     <expand macro="requirements" />
+    <expand macro="xrefs"/>
     <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>
-

tools/tertiary-analysis/garnett/garnett_classify_cells.xml

@@ -4,6 +4,7 @@
         <import>garnett_macros.xml</import>
     </macros>
     <expand macro="requirements" />
+    <expand macro="xrefs"/>
     <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>
-

tools/tertiary-analysis/garnett/garnett_get_feature_genes.xml

@@ -4,6 +4,7 @@
         <import>garnett_macros.xml</import>
     </macros>
     <expand macro="requirements" />
+    <expand macro="xrefs"/>
     <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>

tools/tertiary-analysis/garnett/garnett_get_std_output.xml

@@ -4,6 +4,7 @@
         <import>garnett_macros.xml</import>
     </macros>
     <expand macro="requirements" />
+    <expand macro="xrefs"/>
     <command detect_errors="exit_code"><![CDATA[
         garnett_get_std_output.R --input-object '${input_object}' --classifier '${classifier}' --output-file-path '${output_file_path}'
     ]]></command>
@@ -26,4 +27,4 @@
         @VERSION_HISTORY@
     ]]></help>
      <expand macro="citations" />
-</tool>
+</tool>

tools/tertiary-analysis/garnett/garnett_macros.xml

@@ -2,6 +2,11 @@
     <token name="@TOOL_VERSION@">0.2.8</token>
     <token name="@HELP@">More information can be found at https://cole-trapnell-lab.github.io/garnett/docs/</token>
     <token name="@PROFILE@">18.01</token>
+    <xml name="xrefs">
+      <xrefs>
+          <xref type="bio.tools">Garnett</xref>
+      </xrefs>
+    </xml>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="0.0.5">garnett-cli</requirement>

tools/tertiary-analysis/garnett/garnett_train_classifier.xml

@@ -4,46 +4,47 @@
         <import>garnett_macros.xml</import>
     </macros>
     <expand macro="requirements" />
+    <expand macro="xrefs"/>
     <command detect_errors="exit_code"><![CDATA[
         garnett_train_classifier.R --cds-object '${cds_object}' --marker-file-path '${marker_file_path}' --database '${database}' --cores \${GALAXY_SLOTS:-1} --output-path '${output_classifier_path}'
         #if $train_id
-        --train-id '${train_id}' 
+        --train-id '${train_id}'
         #end if
         #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}' 
+        --marker-file-gene-id-type '${marker_file_gene_id_type}'
         #end if
         #if $num_unknown
-        --num-unknown '${num_unknown}' 
+        --num-unknown '${num_unknown}'
         #end if
         #if $min_observations
-        --min-observations '${min_observations}' 
+        --min-observations '${min_observations}'
         #end if
         #if $max_training_samples
-        --max-training-samples '${max_training_samples}' 
+        --max-training-samples '${max_training_samples}'
         #end if
         #if $propogate_markers
         --propogate-markers '${propogate_markers}'
         #end if
         #if $classifier_gene_id_type
-        --classifier-gene-id-type '${classifier_gene_id_type}' 
+        --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="train_id" label="Dataset ID" help="ID of the training dataset" />
         <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" />
         <param type="text" name="marker_file_gene_id_type" label="Marker gene id type" value="ENSEMBL" help="Format of the gene IDs in your marker file" />
         <param type="integer" name="num_unknown" value='500' label="number of outputs" help="Number of outgroups to compare against" />
-        <param type="integer" name="min_observations" value='8' label="Min num of observations" help="The minimum number of representative cells per 
+        <param type="integer" name="min_observations" value='8' label="Min num of observations" help="The minimum number of representative cells per
         cell type required to include the cell type in the predictive model" />
         <param type="integer" name="max_training_samples" value='500' label="Max num of training samples" help="The maximum number of representative cells per cell
-        type to be included in the model training. Decreasing this number 
+        type to be included in the model training. Decreasing this number
         increases speed, but may hurt performance of the model." />
         <param type="boolean" name="propogate_markers" checked="true" label="propogate markers" help="Should markers from child nodes of a cell type be used
         in finding representatives of the parent type?" />
@@ -65,4 +66,4 @@
         @VERSION_HISTORY@
     ]]></help>
     <expand macro="citations" />
-</tool>
+</tool>

tools/tertiary-analysis/garnett/garnett_transform_markers.xml

@@ -4,6 +4,7 @@
         <import>garnett_macros.xml</import>
     </macros>
     <expand macro="requirements" />
+    <expand macro="xrefs"/>
     <command detect_errors="exit_code"><![CDATA[
         transform_marker_file.R --input-marker-file '${input_marker_file}' --marker-list '${marker_list}'  --garnett-marker-file '${garnett_marker_file}'
 
@@ -45,4 +46,3 @@
     ]]></help>
     <expand macro="citations" />
 </tool>
-

tools/tertiary-analysis/garnett/update_marker_file.xml

@@ -4,6 +4,7 @@
         <import>garnett_macros.xml</import>
     </macros>
     <expand macro="requirements" />
+    <expand macro="xrefs"/>
     <command detect_errors="exit_code"><![CDATA[
         update_marker_file.R --marker-list-obj '${marker_list_obj}' --marker-check-file '${marker_check_file}'    --updated-marker-file '${updated_marker_file}'
 
@@ -39,5 +40,5 @@
 
         @VERSION_HISTORY@
     ]]></help>
-     <expand macro="citations" /> 
-</tool>
+     <expand macro="citations" />
+</tool>

tools/tertiary-analysis/monocle3/monocle3-create.xml

@@ -5,6 +5,7 @@
     <import>monocle3-macros.xml</import>
   </macros>
   <expand macro="requirements"/>
+  <expand macro="xrefs"/>
   <command detect_errors="exit_code"><![CDATA[
 ln -s '${expression_matrix}' expression_matrix.'${expression_matrix_format}' &&
 #if $cell_metadata

tools/tertiary-analysis/monocle3/monocle3-diffExp.xml

@@ -5,6 +5,7 @@
     <import>monocle3-macros.xml</import>
   </macros>
   <expand macro="requirements"/>
+  <expand macro="xrefs"/>
   <command detect_errors="exit_code"><![CDATA[
 LANG=en_US.UTF-8 monocle3 diffExp
     --neighbor-graph '$(neighbor_graph)'

tools/tertiary-analysis/monocle3/monocle3-learnGraph.xml

@@ -5,6 +5,7 @@
     <import>monocle3-macros.xml</import>
   </macros>
   <expand macro="requirements"/>
+  <expand macro="xrefs"/>
   <command detect_errors="exit_code"><![CDATA[
 LANG=en_US.UTF-8 monocle3 learnGraph
 #if $no_partition

tools/tertiary-analysis/monocle3/monocle3-macros.xml

@@ -29,6 +29,12 @@
 #end if
   </token>
 
+  <xml name="xrefs">
+    <xrefs>
+      <xref type="bio.tools">monocle</xref>
+    </xrefs>
+  </xml>
+
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="0.0.7">monocle3-cli</requirement>

tools/tertiary-analysis/monocle3/monocle3-orderCells.xml

@@ -5,6 +5,7 @@
     <import>monocle3-macros.xml</import>
   </macros>
   <expand macro="requirements"/>
+  <expand macro="xrefs"/>
   <command detect_errors="exit_code"><![CDATA[
 LANG=en_US.UTF-8 monocle3 orderCells
     --reduction-method '${reduction_method}'

tools/tertiary-analysis/monocle3/monocle3-partition.xml

@@ -5,6 +5,7 @@
     <import>monocle3-macros.xml</import>
   </macros>
   <expand macro="requirements"/>
+  <expand macro="xrefs"/>
   <command detect_errors="exit_code"><![CDATA[
 LANG=en_US.UTF-8 monocle3 partition
     --reduction-method '${reduction_method}'

tools/tertiary-analysis/monocle3/monocle3-plotCells.xml

@@ -4,6 +4,7 @@
   <macros>
     <import>monocle3-macros.xml</import>
   </macros>
+  <expand macro="xrefs"/>
   <requirements>
     <requirement type="package" version="0.0.9">monocle3-cli</requirement>
   </requirements>

tools/tertiary-analysis/monocle3/monocle3-preprocess.xml

@@ -5,6 +5,7 @@
     <import>monocle3-macros.xml</import>
   </macros>
   <expand macro="requirements"/>
+  <expand macro="xrefs"/>
   <command detect_errors="exit_code"><![CDATA[
 LANG=en_US.UTF-8 monocle3 preprocess
     --method '${method}'

tools/tertiary-analysis/monocle3/monocle3-reduceDim.xml

@@ -5,6 +5,7 @@
     <import>monocle3-macros.xml</import>
   </macros>
   <expand macro="requirements"/>
+  <expand macro="xrefs"/>
   <command detect_errors="exit_code"><![CDATA[
 LANG=en_US.UTF-8 monocle3 reduceDim
 #if $max_components

tools/tertiary-analysis/monocle3/monocle3-topmarkers.xml

@@ -4,6 +4,7 @@
   <macros>
     <import>monocle3-macros.xml</import>
   </macros>
+  <expand macro="xrefs"/>
   <requirements>
     <requirement type="package" version="0.0.8">monocle3-cli</requirement>
   </requirements>

tools/tertiary-analysis/pyscenic/macros.xml

@@ -1,5 +1,10 @@
 <macros>
     <token name="@TOOL_VERSION@">0.12.1</token>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">maaslin2</xref>
+        </xrefs>
+    </xml>
     <xml name="requirements">
         <requirements>
             <container type="docker">

tools/tertiary-analysis/pyscenic/pyscenic_aucell.xml

@@ -4,6 +4,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
+    <expand macro="xrefs"/>
     <command><![CDATA[
         ln -s '${expression_mtx_fname}' expr_mat.loom &&
         ln -s '${signatures_fname}' regulons.tsv &&

tools/tertiary-analysis/pyscenic/pyscenic_binarize_aucell.xml

@@ -4,6 +4,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
+    <expand macro="xrefs"/>
     <command detect_errors="exit_code">
         <![CDATA[
         ln -s $input_file aucell.tsv &&

tools/tertiary-analysis/pyscenic/pyscenic_ctx.xml

@@ -6,6 +6,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
+    <expand macro="xrefs"/>
     <command><![CDATA[
     #set PySCENIC_DB = "db.genes_vs_motifs.rankings.feather"
     ln -s '${module_fname}' tf2targets.tsv &&

tools/tertiary-analysis/pyscenic/pyscenic_grn.xml

@@ -4,6 +4,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
+    <expand macro="xrefs"/>
     <command detect_errors="exit_code">
         <![CDATA[
             ln -s '${expression_mtx}' expr_mat.loom && 

tools/tertiary-analysis/sc3/sc3-calc-biology.xml

@@ -5,6 +5,7 @@
     <import>sc3-macros.xml</import>
   </macros>
   <expand macro="requirements" />
+  <expand macro="xrefs"/>
   <command detect_errors="exit_code"><![CDATA[
 sc3-sc3-calc-biology.R -i '${sc3_consensus}' -o '${sc3_biology_markers}' -t '${sc3_biology_markers_tsv}' -k '${ks}' -r '${regime}'
   ]]></command>

tools/tertiary-analysis/sc3/sc3-calc-consens.xml

@@ -5,6 +5,7 @@
     <import>sc3-macros.xml</import>
   </macros>
   <expand macro="requirements" />
+  <expand macro="xrefs"/>
   <command detect_errors="exit_code"><![CDATA[
 sc3-sc3-calc-consens.R -i '${sc3_kmeans}' -t '${clusters}' -o '${sc3_consensus}'
   ]]></command>

tools/tertiary-analysis/sc3/sc3-calc-dists.xml

@@ -5,6 +5,7 @@
     <import>sc3-macros.xml</import>
   </macros>
   <expand macro="requirements" />
+  <expand macro="xrefs"/>
   <command detect_errors="exit_code"><![CDATA[
 sc3-sc3-calc-dists.R -i '${sc3_prepared}' -o '${sc3_distances}'
   ]]></command>