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comparison edger-repenrich.xml @ 11:6bba3e33c2e7 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 11df9f0b68d35d3a9424a17e4cefee6cfb9d4c19
author artbio
date Sat, 09 Mar 2024 22:32:46 +0000
parents 6f4143893463
children 530626b0757c
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10:6f4143893463 11:6bba3e33c2e7
1 <tool id="edger-repenrich" name="edgeR-repenrich" version="1.5.2"> 1 <tool id="edger-repenrich" name="edgeR-repenrich" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Determines differentially expressed features from RepEnrich counts</description> 2 <description>Determines differentially expressed features from RepEnrich counts</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="3.16.5">bioconductor-edger</requirement> 4 <import>macros.xml</import>
5 <requirement type="package" version="3.30.13">bioconductor-limma</requirement> 5 </macros>
6 <requirement type="package" version="1.20.0">r-getopt</requirement> 6 <expand macro="requirements"/>
7 <requirement type="package" version="0.2.15">r-rjson</requirement>
8 </requirements>
9 <stdio> 7 <stdio>
10 <regex match="Execution halted" 8 <regex match="Execution halted"
11 source="both" 9 source="both"
12 level="fatal" 10 level="fatal"
13 description="Execution halted." /> 11 description="Execution halted." />
107 <data format="tabular" name="counts_out" label="Normalized counts file"> 105 <data format="tabular" name="counts_out" label="Normalized counts file">
108 <filter>normCounts == True</filter> 106 <filter>normCounts == True</filter>
109 </data> 107 </data>
110 </outputs> 108 </outputs>
111 <tests> 109 <tests>
112 <test> 110 <test expect_num_outputs="3">
113 <param name="factorName" value="Genotype"/> 111 <param name="factorName" value="Genotype"/>
114 <param name="factorLevel_A" value="Mutant"/> 112 <param name="factorLevel_A" value="Mutant"/>
115 <param name="countsFiles_A" value="355_fraction_counts.tab,356_fraction_counts.tab"/> 113 <param name="countsFiles_A" value="355_fraction_counts.tab,356_fraction_counts.tab"/>
116 <param name="alignmentFiles_A" value="aligned_355.tab,aligned_356.tab"/> 114 <param name="alignmentFiles_A" value="aligned_355.tab,aligned_356.tab"/>
117 <param name="factorLevel_B" value="Wildtype"/> 115 <param name="factorLevel_B" value="Wildtype"/>