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comparison edger-repenrich.xml @ 3:1805b262c12d draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit ca572343d2a24d645dedd6c5d2cb352115ed8bf3
author drosofff
date Tue, 30 May 2017 10:34:53 -0400
parents aed130b47d36
children d359ec9f0fe1
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2:aed130b47d36 3:1805b262c12d
1 <tool id="edger-repenrich" name="edgeR-repenrich" version="1.0.0"> 1 <tool id="edger-repenrich" name="edgeR-repenrich" version="1.1.0">
2 <description>Determines differentially expressed features from RepEnrich counts</description> 2 <description>Determines differentially expressed features from RepEnrich counts</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.16.5">bioconductor-edger</requirement> 4 <requirement type="package" version="3.16.5">bioconductor-edger</requirement>
5 <requirement type="package" version="3.30.13">bioconductor-limma</requirement> 5 <requirement type="package" version="3.30.13">bioconductor-limma</requirement>
6 <requirement type="package" version="1.20.0">r-getopt</requirement> 6 <requirement type="package" version="1.20.0">r-getopt</requirement>
96 <param name="alignmentFiles_B" type="data" format="tabular" multiple="true" label="Number of aligned reads file(s)" help="files of total aligned reads generated by repenrich"/> 96 <param name="alignmentFiles_B" type="data" format="tabular" multiple="true" label="Number of aligned reads file(s)" help="files of total aligned reads generated by repenrich"/>
97 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false" 97 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
98 label="Output normalized counts table" /> 98 label="Output normalized counts table" />
99 </inputs> 99 </inputs>
100 <outputs> 100 <outputs>
101 <data format="tabular" name="edger_out" label="edgeR result file on ${on_string}"> 101 <data format="tabular" name="edger_out" label="edgeR: ${factorLevel_A} compared to ${factorLevel_B}">
102 <actions> 102 <actions>
103 <action name="column_names" type="metadata" default="Tag,log2(FC),FDR,Class,Type" /> 103 <action name="column_names" type="metadata" default="Tag,log2(FC),FDR,Class,Type" />
104 </actions> 104 </actions>
105 </data> 105 </data>
106 <data format="pdf" name="plots" label="edgeR plots on ${on_string}" /> 106 <data format="pdf" name="plots" label="edgeR plots" />
107 <data format="tabular" name="counts_out" label="Normalized counts file on ${on_string}"> 107 <data format="tabular" name="counts_out" label="Normalized counts file">
108 <filter>normCounts == True</filter> 108 <filter>normCounts == True</filter>
109 </data> 109 </data>
110 </outputs> 110 </outputs>
111 <tests> 111 <tests>
112 <test> 112 <test>
113 <param name="factorName" value="genotype"/> 113 <param name="factorName" value="Genotype"/>
114 <param name="factorLevel_A" value="wildtype"/> 114 <param name="factorLevel_A" value="Mutant"/>
115 <param name="countsFiles_A" value="353_fraction_counts.tab,354_fraction_counts.tab"/> 115 <param name="countsFiles_A" value="355_fraction_counts.tab,356_fraction_counts.tab"/>
116 <param name="alignmentFiles_A" value="aligned_353.tab,aligned_354.tab"/> 116 <param name="alignmentFiles_A" value="aligned_355.tab,aligned_356.tab"/>
117 <param name="factorLevel_B" value="mutant"/> 117 <param name="factorLevel_B" value="Wildtype"/>
118 <param name="countsFiles_B" value="355_fraction_counts.tab,356_fraction_counts.tab"/> 118 <param name="countsFiles_B" value="353_fraction_counts.tab,354_fraction_counts.tab"/>
119 <param name="alignmentFiles_B" value="aligned_355.tab,aligned_356.tab"/> 119 <param name="alignmentFiles_B" value="aligned_353.tab,aligned_354.tab"/>
120 <param name="normCounts" value="True"/> 120 <param name="normCounts" value="True"/>
121 <output name="counts_out" file="Normalized_counts_file.tab"/> 121 <output name="counts_out" file="Normalized_counts_file.tab"/>
122 <output name="plots" file="edgeR_plots.pdf"/> 122 <output name="plots" file="edgeR_plots.pdf"/>
123 <output name="edger_out" file="edgeR_result_file.tab"/> 123 <output name="edger_out" file="edgeR_result_file.tab"/>
124 124