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comparison galaxy/wrappers/FormatForGSEA.xml @ 1:d72f1bc5ce9e draft

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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
author vandelj
date Wed, 09 Sep 2020 10:36:26 +0000
parents 3022feec50fe
children
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0:3022feec50fe 1:d72f1bc5ce9e
1 <tool name="GIANT-GSEA Formatting" id="giant_gsea_format" version="0.2.0"> 1 <tool name="GIANT-GSEA Formatting" id="giant_gsea_format" version="0.2.0">
2 <description>Format input files for GSEA software</description> 2 <description>Format input files for GSEA software</description>
3 <code file="../../src/General_functions.py"/> 3 <code file="../../src/General_functions.py"/>
4 <!--<code file="./src/General_functions.py"/> change for Planemo test-->
4 <stdio> 5 <stdio>
5 <regex match="Execution halted" 6 <regex match="Execution halted"
6 source="both" 7 source="both"
7 level="fatal" 8 level="fatal"
8 description="Execution halted." /> 9 description="Execution halted." />
58 <when value="classicGSEA"> 59 <when value="classicGSEA">
59 <param type="data" name="expressionData" format="tabular" label="Normalized expression tabular file" optional="false" multiple="false"> 60 <param type="data" name="expressionData" format="tabular" label="Normalized expression tabular file" optional="false" multiple="false">
60 </param> 61 </param>
61 <param type="data" name="conditionInformation" format="tabular" label="Factor information tabular file" optional="false" multiple="false"> 62 <param type="data" name="conditionInformation" format="tabular" label="Factor information tabular file" optional="false" multiple="false">
62 </param> 63 </param>
63 <param name="factorToInclude" type="select" label="Reference factor" multiple="false" optional="false" refresh_on_change="true" 64 <param name="factorToInclude" type="select" label="Reference factor" multiple="false" optional="false" refresh_on_change="true"
64 dynamic_options="get_column_names_filteredList(mainCondition['conditionInformation'].file_name,[0])"> 65 dynamic_options="get_column_names_filteredList(mainCondition['conditionInformation'].file_name,[0])">
65 </param> 66 </param>
66 </when> 67 </when>
67 <when value="rankedGSEA"> 68 <when value="rankedGSEA">
68 <param type="data" name="differentialAnalysis" format="tabular" label="Differential analysis tabular file (as given by LIMMA diff.exp. tool)" multiple="false" help="This file should contain only annotated gene names or only probe identifiers as rows but no both kinds."> 69 <param type="data" name="differentialAnalysis" format="tabular" label="Differential analysis tabular file (as given by LIMMA diff.exp. tool)" multiple="false" help="This file should contain only annotated gene names or only probe identifiers as rows but no both kinds.">
99 <data format="txt" name="log" label="${title}_Log" /> 100 <data format="txt" name="log" label="${title}_Log" />
100 </outputs> 101 </outputs>
101 102
102 <tests> 103 <tests>
103 <test maxseconds="3600" > 104 <test maxseconds="3600" >
104 <param name="selection" value="classicGSEA" /> 105 <conditional name="mainCondition">
105 <param name="expressionData" value="./NormalizedData.tabular" /> 106 <param name="selection" value="classicGSEA" />
106 <param name="conditionInformation" value="./conditionGroups.txt" /> 107 <param name="expressionData" value="./NormalizedData.tabular" />
107 <param name="factorToInclude" value="Treatment" /> 108 <param name="conditionInformation" value="./FactorFileGenerator/output/conditionsFile.csv" />
108 <output name="outExpression" file="./GSEA-Formatting/outputExpression.gct" /> 109 <param name="factorToInclude" value="Treatment" />
109 <output name="outPhenotypes" file="./GSEA-Formatting/outputPhenotypesTreatment.cls" /> 110 </conditional>
110 <output name="log" file="./GSEA-Formatting/outputRanks.log" /> 111 <output name="outExpression" file="./FormatForGSEA/output/outputExpression_A.gct" />
112 <output name="outPhenotypes" file="./FormatForGSEA/output/outputPhenotypes_A.cls" />
113 <output name="log" file="./FormatForGSEA/output/outputLog_A.txt" />
111 </test> 114 </test>
115
112 <test maxseconds="3600" > 116 <test maxseconds="3600" >
113 <param name="selection" value="classicGSEA" /> 117 <conditional name="mainCondition">
114 <param name="expressionData" value="./NormalizedData.tabular" /> 118 <param name="selection" value="rankedGSEA" />
115 <param name="conditionInformation" value="./conditionGroups.txt" /> 119 <param name="differentialAnalysis" value="./DiffExprLimma/output/outputStat.csv" />
116 <param name="factorToInclude" value="Type" /> 120 <param name="comparisonsToUse" value="TreatVsControl" />
117 <output name="outExpression" file="./GSEA-Formatting/outputExpression.gct" /> 121 <param name="rankingIndice" value="absFC" />
118 <output name="outPhenotypes" file="./GSEA-Formatting/outputPhenotypesType.cls" /> 122 <param name="pvalThreshold" value="0.05" />
119 <output name="log" file="./GSEA-Formatting/outputRanks.log" /> 123 </conditional>
120 </test> 124 <output name="outRankedGenes" file="./FormatForGSEA/output/outputRanks_B.rnk" />
121 <test maxseconds="3600" > 125 <output name="log" file="./FormatForGSEA/output/outputLog_B.txt" />
122 <param name="selection" value="rankedGSEA" />
123 <param name="differentialAnalysis" value="./LIMMAstatistics.tabular" />
124 <param name="comparisonsToUse" value="WT*Control-KO*Control" />
125 <param name="rankingIndice" value="FC" />
126 <param name="pvalThreshold" value="0.05" />
127 <output name="outRankedGenes" file="./GSEA-Formatting/outputRanks.rnk" />
128 <output name="log" file="./GSEA-Formatting/outputRanks.log" />
129 </test> 126 </test>
130 </tests> 127 </tests>
131 <help> 128 <help>
132 <![CDATA[ 129 <![CDATA[
133 **What it does** 130 **What it does**