Mercurial > repos > bimib > marea
diff Marea/marea.xml @ 47:3af9d394367c draft
Uploaded
| author | bimib |
|---|---|
| date | Wed, 19 Feb 2020 10:44:52 -0500 |
| parents | 7b1971251c63 |
| children | e4235b5231e4 |
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--- a/Marea/marea.xml Wed Jan 22 11:50:54 2020 -0500 +++ b/Marea/marea.xml Wed Feb 19 10:44:52 2020 -0500 @@ -1,28 +1,19 @@ -<tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.6"> - <description></description> - <macros> - <import>marea_macros.xml</import> - </macros> - <requirements> - <requirement type="package" version="0.23.0">pandas</requirement> - <requirement type="package" version="1.1.0">scipy</requirement> - <requirement type="package" version="0.10.1">cobra</requirement> - <requirement type="package" version="4.2.1">lxml</requirement> - <requirement type="package" version="0.8.1">svglib</requirement> - <requirement type="package" version="3.4.0">reportlab</requirement> - </requirements> - <command detect_errors="exit_code"> - <![CDATA[ +<tool id="MaREA" name="Metabolic Reaction Enrichment Analysis" version="1.0.7"> + <macros> + <import>marea_macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="0.23.0">pandas</requirement> + <requirement type="package" version="1.1.0">scipy</requirement> + <requirement type="package" version="0.10.1">cobra</requirement> + <requirement type="package" version="4.2.1">lxml</requirement> + <requirement type="package" version="0.8.1">svglib</requirement> + <requirement type="package" version="3.4.0">reportlab</requirement> + </requirements> + <command detect_errors="exit_code"> + <![CDATA[ python $__tool_directory__/marea.py - --rules_selector $cond_rule.rules_selector - #if $cond_rule.rules_selector == 'Custom': - --custom ${cond_rule.Custom_rules} - --yes_no ${cond_rule.cond_map.yes_no} - #if $cond_rule.cond_map.yes_no == 'yes': - --custom_map $cond_rule.cond_map.Custom_map - #end if - #end if - + --tool_dir $__tool_directory__ --option $cond.type_selector --out_log $log @@ -36,153 +27,130 @@ #for $data in $cond.input_Datasets: ${data.input_name} #end for + --comparison ${cond.comparis.comparison} #if $cond.advanced.choice == 'true': - --none ${cond.advanced.None} - --pValue ${cond.advanced.pValue} - --fChange ${cond.advanced.fChange} - --generate_svg ${cond.advanced.generateSvg} - --generate_pdf ${cond.advanced.generatePdf} - --generate_ras ${cond.advanced.generateRas} - #else - --none true - --pValue 0.05 - --fChange 1.5 - --generate_svg false - --generate_pdf true - --generate_ras false - #end if + --pValue ${cond.advanced.pValue} + --fChange ${cond.advanced.fChange} + --generate_svg ${cond.advanced.generateSvg} + --generate_pdf ${cond.advanced.generatePdf} + #else + --pValue 0.05 + --fChange 1.5 + --generate_svg false + --generate_pdf true + --generate_ras false + #end if #elif $cond.type_selector == 'dataset_class': --input_data ${input_data} --input_class ${input_class} + --comparison ${cond.comparis.comparison} + #if $cond.comparis.comparison == 'onevsmany' + --control ${cond.comparis.controlgroup} + #end if #if $cond.advanced.choice == 'true': - --none ${cond.advanced.None} - --pValue ${cond.advanced.pValue} - --fChange ${cond.advanced.fChange} - --generate_svg ${cond.advanced.generateSvg} - --generate_pdf ${cond.advanced.generatePdf} - --generate_ras ${cond.advanced.generateRas} - #else - --none true - --pValue 0.05 - --fChange 1.5 - --generate_svg false - --generate_pdf true - --generate_ras false - #end if - #end if - #if $cond.type_selector == 'datasets_rasonly': - --input_datas ${input_Datasets} - --single_ras_file $ras_single - --none ${cond.None} + --pValue ${cond.advanced.pValue} + --fChange ${cond.advanced.fChange} + --generate_svg ${cond.advanced.generateSvg} + --generate_pdf ${cond.advanced.generatePdf} + #else + --pValue 0.05 + --fChange 1.5 + --generate_svg false + --generate_pdf true + #end if #end if ]]> - </command> - - <inputs> - <conditional name="cond_rule"> - <expand macro="options"/> - <when value="HMRcore"> - </when> - <when value="Recon"> - </when> - <when value="Custom"> - <param name="Custom_rules" type="data" format="tabular, csv, tsv, xml" label="Custom rules" /> - <conditional name="cond_map"> - <param name="yes_no" type="select" label="Custom map? (optional)"> - <option value="no" selected="true">no</option> - <option value="yes">yes</option> - </param> - <when value="yes"> - <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/> - </when> - <when value="no"> - </when> - </conditional> - </when> - </conditional> - <conditional name="cond"> - <param name="type_selector" argument="--option" type="select" label="Input format:"> - <option value="datasets" selected="true">RNAseq of group 1 + RNAseq of group 2 + ... + RNAseq of group N</option> - <option value="dataset_class">RNAseq of all samples + sample group specification</option> - <option value="datasets_rasonly" selected="true">RNAseq dataset</option> - </param> - <when value="datasets"> - <repeat name="input_Datasets" title="RNAseq" min="2"> - <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" /> - <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" /> - </repeat> - <conditional name="advanced"> + </command> + <inputs> + <conditional name="cond"> + <param name="type_selector" argument="--option" type="select" label="Input format:"> + <option value="datasets" selected="true">RAS of group 1 + RAS of group 2 + ... + RAS of group N</option> + <option value="dataset_class">RAS of all samples + sample group specification</option> + </param> + <when value="datasets"> + <repeat name="input_Datasets" title="RAS dataset" min="2"> + <param name="input" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" /> + <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" /> + </repeat> + <conditional name="comparis"> + <param name="comparison" argument="--comparison" type="select" label="Groups comparison:"> + <option value="manyvsmany" selected="true">One vs One</option> + <option value="onevsrest">One vs All</option> + <option value="onevsmany">One vs Control</option> + </param> + <when value="onevsmany"> + <param name="controlgroup" argument="--controlgroup" type="text" label="Control group label:" value="0" help="Name of group label to be compared to others"/> + </when> + </conditional> + <conditional name="advanced"> <param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom parameters for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps."> - <option value="true" selected="true">No</option> - <option value="false">Yes</option> + <option value="true" selected="true">No</option> + <option value="false">Yes</option> </param> - <when value="false"> - </when> + <when value="false"></when> <when value="true"> - <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> - <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" /> - <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" /> - <param name="generateSvg" argument="--generateSvg" type="boolean" checked="false" label="Generate SVG map" help="should the program generate an editable svg map of the processes?" /> - <param name="generatePdf" argument="--generatePdf" type="boolean" checked="true" label="Generate PDF map" help="should the program return a non editable (but displayble) pdf map of the processes?" /> - <param name="generateRas" argument="--generateRas" type="boolean" checked="false" label="Generate Reaction Activity Score for each table" help="Generate Reaction Activity Score for each table" /> + <conditional name="cond_map"> + <param name="choice" type="boolean" checked="false" label="Use custom map?" help="Use this option only if you have generated RAS using a custom set of rules"> + <option value="false" selected="true">No</option> + <option value="true">Yes</option> + </param> + <when value="true"> + <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/> + </when> + </conditional> + <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" /> + <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" /> + <param name="generateSvg" argument="--generateSvg" type="boolean" checked="false" label="Generate SVG map" help="should the program generate an editable svg map of the processes?" /> + <param name="generatePdf" argument="--generatePdf" type="boolean" checked="true" label="Generate PDF map" help="should the program return a non editable (but displayble) pdf map of the processes?" /> </when> - </conditional> - </when> - <when value="datasets_rasonly"> - <param name="input_Datasets" argument="--input_datas" type="data" format="tabular, csv, tsv" label="add dataset" /> - <param name="input_name" argument="--names" type="text" label="Dataset's name:" value="Dataset" help="Default: Dataset" /> - <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> - </when> - <when value="dataset_class"> - <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RNAseq of all samples" /> + </conditional> + </when> + <when value="dataset_class"> + <param name="input_data" argument="--input_data" type="data" format="tabular, csv, tsv" label="RAS of all samples" /> <param name="input_class" argument="--input_class" type="data" format="tabular, csv, tsv" label="Sample group specification" /> - <conditional name="advanced"> - <param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom parameters for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps."> - <option value="true" selected="true">No</option> - <option value="false">Yes</option> + <conditional name="comparis"> + <param name="comparison" argument="--comparison" type="select" label="Groups comparison:"> + <option value="manyvsmany" selected="true">One vs One</option> + <option value="onevsrest">One vs All</option> + <option value="onevsmany">One vs Control</option> </param> - <when value="false"> - </when> - <when value="true"> - <param name="None" argument="--none" type="boolean" truevalue="true" falsevalue="false" checked="true" label="(A and NaN) solved as (A)?" /> - <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" /> - <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" /> - <param name="generateSvg" argument="--generateSvg" type="boolean" checked="false" label="Generate SVG map" help="should the program generate an editable svg map of the processes?" /> - <param name="generatePdf" argument="--generatePdf" type="boolean" checked="true" label="Generate PDF map" help="should the program return a non editable (but displayble) pdf map of the processes?" /> - <param name="generateRas" argument="--generateRas" type="boolean" checked="false" label="Generate Reaction Activity Score for each table" help="Generate Reaction Activity Score for each table" /> + <when value="onevsmany"> + <param name="controlgroup" argument="--controlgroup" type="text" label="Control group label:" value="0" help="Name of group label to be compared to others"/> </when> - </conditional> - </when> - </conditional> - - - - - </inputs> - - <outputs> - <data format="txt" name="log" label="MaREA - Log" /> - <data format="tabular" name="ras_single" label="MaREA - RAS - ${cond.input_name}"> - <filter>cond['type_selector'] == "datasets_rasonly"</filter> - </data> - <collection name="results" type="list" label="MaREA - Results"> - <filter>cond['type_selector'] == "datasets" or cond['type_selector'] == "dataset_class"</filter> - <discover_datasets pattern="__name_and_ext__" directory="result"/> - </collection> - <collection name="ras" type="list" label="MaREA - RAS list" format_source="tabular"> - <filter>cond['type_selector'] != "datasets_rasonly" and cond['advanced']['choice'] and cond['advanced']['generateRas']</filter> - <discover_datasets pattern="__name_and_ext__" directory="ras" format="tabular"/> + </conditional> + <conditional name="advanced"> + <param name="choice" type="boolean" checked="false" label="Use advanced options?" help="Use this options to choose custom parameters for evaluation: pValue, Fold-Change threshold, how to solve (A and NaN) and specify output maps."> + <option value="true" selected="true">No</option> + <option value="false">Yes</option> + </param> + <when value="false"></when> + <when value="true"> + <conditional name="cond_map"> + <param name="choice" type="boolean" checked="false" label="Use custom map?" help="Use this option only if you have generated RAS using a custom set of rules"> + <option value="false" selected="true">No</option> + <option value="true">Yes</option> + </param> + <when value="true"> + <param name="Custom_map" argument="--custom_map" type="data" format="xml, svg" label="custom-map.svg"/> + </when> + </conditional> + <param name="pValue" argument="--pValue" type="float" size="20" value="0.01" max="1" min="0" label="P-value threshold:" help="min value 0" /> + <param name="fChange" argument="--fChange" type="float" size="20" value="1.2" min="1" label="Fold-Change threshold:" help="min value 1" /> + <param name="generateSvg" argument="--generateSvg" type="boolean" checked="false" label="Generate SVG map" help="should the program generate an editable svg map of the processes?" /> + <param name="generatePdf" argument="--generatePdf" type="boolean" checked="true" label="Generate PDF map" help="should the program return a non editable (but displayble) pdf map of the processes?" /> + </when> + </conditional> + </when> + </conditional> +</inputs> +<outputs> + <data format="txt" name="log" label="MaREA - Log" /> + <collection name="results" type="list" label="MaREA - Results"> + <discover_datasets pattern="__name_and_ext__" directory="result"/> </collection> - - </outputs> - <tests> - <test> - <param name="pValue" value="0.56"/> - <output name="log" file="log.txt"/> - </test> - </tests> - <help> -<![CDATA[ +</outputs> +<help> + <![CDATA[ What it does ------------- @@ -268,7 +236,6 @@ .. _MaREA cluster analysis: http://link del tool di cluster.org ]]> - </help> - <expand macro="citations" /> -</tool> +</help> +<expand macro="citations" />undefined</tool>