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comparison dexseq.xml @ 8:2872c633f07e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit d6fb005b0dbf26037aab1748d9b5df12876c674d"
author iuc
date Sun, 19 Dec 2021 23:02:46 +0000
parents 278b189248cd
children df929f257179
comparison
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7:62adf13b86ea 8:2872c633f07e
1 <tool id="dexseq" name="DEXSeq" version="@VERSION@+galaxy1"> 1 <tool id="dexseq" name="DEXSeq" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
2 <description>Determines differential exon usage from count tables</description> 2 <description>Determines differential exon usage from count tables</description>
3 <xrefs>
4 <xref type="bio.tools">dexseq</xref>
5 </xrefs>
3 <macros> 6 <macros>
4 <import>macros.xml</import> 7 <import>macros.xml</import>
5 </macros> 8 </macros>
6 <expand macro="requirements"> 9 <expand macro="requirements">
7 <requirement type="package" version="1.20.2">r-getopt</requirement> 10 <requirement type="package" version="1.20.2">r-getopt</requirement>
97 <param name="rds" type="boolean" truevalue="True" falsevalue="False" checked="false" 100 <param name="rds" type="boolean" truevalue="True" falsevalue="False" checked="false"
98 label="Output rds file for plotDEXSeq?" help="Can be used to generate plots for individual genes with plotDEXSeq" /> 101 label="Output rds file for plotDEXSeq?" help="Can be used to generate plots for individual genes with plotDEXSeq" />
99 <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.05" label="All the genes under this FDR threshold will be shown in the html report"/> 102 <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.05" label="All the genes under this FDR threshold will be shown in the html report"/>
100 </inputs> 103 </inputs>
101 <outputs> 104 <outputs>
102 <data name="dexseq_out" format="tabular" label="DEXSeq result file on ${on_string}" /> 105 <data name="dexseq_out" format="tabular" label="${tool.name} on ${on_string}: result" />
103 <data name="htmlreport" format="html" label="DEXSeq report on ${on_string}"> 106 <data name="htmlreport" format="html" label="${tool.name} on ${on_string}: report">
104 <filter>report is True</filter> 107 <filter>report is True</filter>
105 </data> 108 </data>
106 <data name="rds_out" format="rdata" from_work_dir="DEXSeqResults.rds" label="DEXSeq rds file on ${on_string}"> 109 <data name="rds_out" format="rds" from_work_dir="DEXSeqResults.rds" label="${tool.name} on ${on_string}: rds file">
107 <filter>rds is True</filter> 110 <filter>rds is True</filter>
108 </data> 111 </data>
109 </outputs> 112 </outputs>
110 <tests> 113 <tests>
111 <!-- Ensure default output works--> 114 <!-- Ensure default output works-->
169 </repeat> 172 </repeat>
170 <param name="report" value="False"/> 173 <param name="report" value="False"/>
171 <param name="rds" value="True"/> 174 <param name="rds" value="True"/>
172 <param name="fdr_cutoff" value="0.05"/> 175 <param name="fdr_cutoff" value="0.05"/>
173 <output name="dexseq_out" ftype="tabular" file="dexseq_result.tabular" compare="sim_size"/> 176 <output name="dexseq_out" ftype="tabular" file="dexseq_result.tabular" compare="sim_size"/>
174 <output name="rds_out" ftype="rdata" file="dexseq.rds" compare="sim_size"/> 177 <output name="rds_out" ftype="rds" file="dexseq.rds" compare="sim_size"/>
175 </test> 178 </test>
176 </tests> 179 </tests>
177 <help><![CDATA[ 180 <help><![CDATA[
178 .. class:: infomark 181 .. class:: infomark
179 182