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comparison dexseq.xml @ 17:d104044e4257 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2ea27822b171dbf519509dc1da150c8ccee2a140
author iuc
date Tue, 04 Apr 2023 08:25:36 +0000
parents 781f60a0c658
children
comparison
equal deleted inserted replaced
16:661f29c77bb0 17:d104044e4257
1 <tool id="dexseq" name="DEXSeq" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> 1 <tool id="dexseq" name="DEXSeq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" 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>
6 <macros> 3 <macros>
7 <import>macros.xml</import> 4 <import>macros.xml</import>
8 </macros> 5 </macros>
9 <expand macro="requirements"> 6 <expand macro="xrefs"/>
10 <requirement type="package" version="1.20.2">r-getopt</requirement> 7 <expand macro="requirements"/>
11 <requirement type="package" version="0.2.20">r-rjson</requirement>
12 </expand>
13 <code file="dexseq_helper.py" /> 8 <code file="dexseq_helper.py" />
14 <stdio> 9 <stdio>
15 <regex match="Execution halted" 10 <regex match="Execution halted"
16 source="both" 11 source="both"
17 level="fatal" 12 level="fatal"
100 <param name="rds" type="boolean" truevalue="True" falsevalue="False" checked="false" 95 <param name="rds" type="boolean" truevalue="True" falsevalue="False" checked="false"
101 label="Output rds file for plotDEXSeq?" help="Can be used to generate plots for individual genes with plotDEXSeq" /> 96 label="Output rds file for plotDEXSeq?" help="Can be used to generate plots for individual genes with plotDEXSeq" />
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"/> 97 <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"/>
103 </inputs> 98 </inputs>
104 <outputs> 99 <outputs>
105 <data name="dexseq_out" format="tabular" label="${tool.name} on ${on_string}: result" /> 100 <data name="dexseq_out" format="tabular" label="${tool.name} on ${on_string}: result">
101 <actions>
102 <action name="column_names" type="metadata" default="GeneID,ExonID,Exon base mean,Dispersion,Stat,p-value,p-adj,X1_group1,X2_group2,log2(FC),Chr. name,Start,End,Width,Strand,Raw counts"/>
103 </actions>
104 </data>
106 <data name="htmlreport" format="html" label="${tool.name} on ${on_string}: report"> 105 <data name="htmlreport" format="html" label="${tool.name} on ${on_string}: report">
107 <filter>report is True</filter> 106 <filter>report is True</filter>
108 </data> 107 </data>
109 <data name="rds_out" format="rds" from_work_dir="DEXSeqResults.rds" label="${tool.name} on ${on_string}: rds file"> 108 <data name="rds_out" format="rds" from_work_dir="DEXSeqResults.rds" label="${tool.name} on ${on_string}: rds file">
110 <filter>rds is True</filter> 109 <filter>rds is True</filter>