Mercurial > repos > proteore > proteore_go_terms_enrich_comparison
diff GO_terms_enrich_comparison.xml @ 7:2e7245bd643d draft default tip
"planemo upload commit 373a85c4179ac6b5cfc77013eab020badb8c8370-dirty"
| author | proteore |
|---|---|
| date | Tue, 04 Feb 2020 05:16:19 -0500 |
| parents | f53249651add |
| children |
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--- a/GO_terms_enrich_comparison.xml Thu Jan 23 03:16:11 2020 -0500 +++ b/GO_terms_enrich_comparison.xml Tue Feb 04 05:16:19 2020 -0500 @@ -1,201 +1,201 @@ -<tool id="go_terms_enrich_comparison" name="GO terms enrich comparison " version="2020.01.23"> - <description>(Human, Mouse, Rat)[clusterProfiler]</description> - <requirements> - <requirement type="package">R</requirement> - <requirement type="package" version="3.8.2">bioconductor-org.hs.eg.db</requirement> - <requirement type="package" version="3.8.2">bioconductor-org.mm.eg.db</requirement> - <requirement type="package" version="3.8.2">bioconductor-org.rn.eg.db</requirement> - <requirement type="package" version="3.10.2">bioconductor-dose</requirement> - <requirement type="package" version="3.12.0">bioconductor-clusterprofiler</requirement> - </requirements> - <command detect_errors="exit_code"><![CDATA[ - - - Rscript $__tool_directory__/GO_terms_enrich_comparison.R - - --nb=$len($lists) - - #for $index, $list in enumerate($lists) - - #if $list.input.ids == "file" - --input.$index="$list.input.file" --name.$index="$list.list_name" --inputtype.$index="file" --header.$index="$list.input.header" --column.$index="$list.input.ncol" - #else - --input.$index="$list.input.txt" --name.$index="$list.list_name" --inputtype.$index="text" - #end if - - #end for - - --org="$species" - --ont="$ontology" - - - > $log - - - ]]></command> - <inputs> - - <repeat name="lists" title="List to compare" min="2" max="5" > - - <conditional name="input" > - <param name="ids" type="select" label="Enter your ID list (Entrez gene ID, e.g. 2810)" help="Copy/paste or from a file (e.g. table)" > - <option value="text">Copy/paste your IDs</option> - <option value="file" selected="true">Input file containing your list of IDs</option> - </param> - <when value="text" > - <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by spaces into the form field, for example: 2810 7534' > - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - </valid> - <mapping initial="none"> - <add source="'" target="__sq__"/> - </mapping> - </sanitizer> - </param> - </when> - <when value="file" > - <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" /> - <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> - <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'> - <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> - </param> - </when> - </conditional> - - <param name="list_name" type="text" label="name of your list" value="List" optional="false"> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - </valid> - <mapping initial="none"> - <add source="'" target="__sq__"/> - </mapping> - </sanitizer> - <validator type="regex" message="Please enter a list name">[a-zA-Z0-9._-]+</validator> - </param> - - </repeat> - - <param name="species" type="select" label="Species" > - <option value="org.Hs.eg.db">Human (Homo sapiens) </option> - <option value="org.Mm.eg.db">Mouse (Mus musculus) </option> - <option value="org.Rn.eg.db">Rat (Rattus norvegicus)</option> - </param> - <param name="ontology" type="select" display="checkboxes" multiple="true" label="Select GO terms category" optional="false" > - <option value="CC">Cellular Component</option> - <option value="BP">Biological Process</option> - <option value="MF">Molecular Function</option> - </param> - </inputs> - - <outputs> - <data name="log" format="txt" label="GO enrich comparison" /> - <collection type="list" label="GO enrichComparison results Table" name="text_output"> - <discover_datasets pattern="(?P<designation>.+\.tsv)" ext="tsv"/> - </collection> - <collection type="list" label="GO enrichComparison results Diagram" name="graph_output" > - <discover_datasets pattern="(?P<designation>.+.png)" ext="png" /> - </collection> - </outputs> - - <tests> - <test> - <repeat name="lists"> - <conditional name="input"> - <param name="ids" value="file" /> - <param name="file" value="Gene_ID_BreastUp.txt" /> - <param name="header" value="true" /> - <param name="ncol" value="c7" /> - <param name="name" value="UP" /> - </conditional> - </repeat> - <repeat name="lists"> - <conditional name="input"> - <param name="ids" value="file" /> - <param name="file" value="Gene_ID_BreastDn.txt" /> - <param name="header" value="true" /> - <param name="ncol" value="c7" /> - <param name="name" value="DN" /> - </conditional> - </repeat> - - <param name="species" value="org.Hs.eg.db"/> - <param name="ontology" value="BP"/> - <output name="log" file="log.txt" /> - <output_collection name="text_output"> - <element name="GO_enrich_comparison_BP.tsv" file="GO_enrich_comparison_BP.tsv" ftype="tsv"/> - </output_collection> - <output_collection name="graph_output"> - <element name="GO_enrich_comparison_BP.png" file="GO_enrich_comparison_BP.png" ftype="png"/> - </output_collection> - </test> - </tests> - <help>< - -User manual / Documentation of the clusterProfiler R package (functions and parameters): -https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html - ------ - -.. class:: infomark - -**Galaxy integration** - -Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR - -David Christiany, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR - -This work has been partially funded through the French National Agency for Research (ANR) IFB project. - -Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. - - - ]]></help> - <citations> - </citations> -</tool> +<tool id="go_terms_enrich_comparison" name="Biological theme comparison" version="2020.02.04"> + <description>(Human, Mouse, Rat)[clusterProfiler]</description> + <requirements> + <requirement type="package">R</requirement> + <requirement type="package" version="3.8.2">bioconductor-org.hs.eg.db</requirement> + <requirement type="package" version="3.8.2">bioconductor-org.mm.eg.db</requirement> + <requirement type="package" version="3.8.2">bioconductor-org.rn.eg.db</requirement> + <requirement type="package" version="3.10.2">bioconductor-dose</requirement> + <requirement type="package" version="3.12.0">bioconductor-clusterprofiler</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + + + Rscript $__tool_directory__/GO_terms_enrich_comparison.R + + --nb=$len($lists) + + #for $index, $list in enumerate($lists) + + #if $list.input.ids == "file" + --input.$index="$list.input.file" --name.$index="$list.list_name" --inputtype.$index="file" --header.$index="$list.input.header" --column.$index="$list.input.ncol" + #else + --input.$index="$list.input.txt" --name.$index="$list.list_name" --inputtype.$index="text" + #end if + + #end for + + --org="$species" + --ont="$ontology" + + + > $log + + + ]]></command> + <inputs> + + <repeat name="lists" title="List to compare" min="2" max="5" > + + <conditional name="input" > + <param name="ids" type="select" label="Enter your ID list (Entrez gene ID, e.g. 2810)" help="Copy/paste or from a file (e.g. table)" > + <option value="text">Copy/paste your IDs</option> + <option value="file" selected="true">Input file containing your list of IDs</option> + </param> + <when value="text" > + <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by spaces into the form field, for example: 2810 7534' > + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + </when> + <when value="file" > + <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" /> + <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" /> + <param name="ncol" type="text" value="c1" label="Column number of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on'> + <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> + </param> + </when> + </conditional> + + <param name="list_name" type="text" label="name of your list" value="List" optional="false"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + <validator type="regex" message="Please enter a list name">[a-zA-Z0-9._-]+</validator> + </param> + + </repeat> + + <param name="species" type="select" label="Species" > + <option value="org.Hs.eg.db">Human (Homo sapiens) </option> + <option value="org.Mm.eg.db">Mouse (Mus musculus) </option> + <option value="org.Rn.eg.db">Rat (Rattus norvegicus)</option> + </param> + <param name="ontology" type="select" display="checkboxes" multiple="true" label="Select GO terms category" optional="false" > + <option value="CC">Cellular Component</option> + <option value="BP">Biological Process</option> + <option value="MF">Molecular Function</option> + </param> + </inputs> + + <outputs> + <data name="log" format="txt" label="GO enrich comparison" /> + <collection type="list" label="GO enrichComparison results Table" name="text_output"> + <discover_datasets pattern="(?P<designation>.+\.tsv)" ext="tsv"/> + </collection> + <collection type="list" label="GO enrichComparison results Diagram" name="graph_output" > + <discover_datasets pattern="(?P<designation>.+.png)" ext="png" /> + </collection> + </outputs> + + <tests> + <test> + <repeat name="lists"> + <conditional name="input"> + <param name="ids" value="file" /> + <param name="file" value="Gene_ID_BreastUp.txt" /> + <param name="header" value="true" /> + <param name="ncol" value="c7" /> + <param name="name" value="UP" /> + </conditional> + </repeat> + <repeat name="lists"> + <conditional name="input"> + <param name="ids" value="file" /> + <param name="file" value="Gene_ID_BreastDn.txt" /> + <param name="header" value="true" /> + <param name="ncol" value="c7" /> + <param name="name" value="DN" /> + </conditional> + </repeat> + + <param name="species" value="org.Hs.eg.db"/> + <param name="ontology" value="BP"/> + <output name="log" file="log.txt" /> + <output_collection name="text_output"> + <element name="GO_enrich_comparison_BP.tsv" file="GO_enrich_comparison_BP.tsv" ftype="tsv"/> + </output_collection> + <output_collection name="graph_output"> + <element name="GO_enrich_comparison_BP.png" file="GO_enrich_comparison_BP.png" ftype="png"/> + </output_collection> + </test> + </tests> + <help>< + +User manual / Documentation of the clusterProfiler R package (functions and parameters): +https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html + +----- + +.. class:: infomark + +**Galaxy integration** + +Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR + +David Christiany, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR + +This work has been partially funded through the French National Agency for Research (ANR) IFB project. + +Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. + + + ]]></help> + <citations> + </citations> +</tool>