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comparison edger.xml @ 10:df0c8d0a5992 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 38cf93fd693c810b4150c5d8aa3763aebc988b07"
author iuc
date Mon, 29 Nov 2021 11:04:53 +0000
parents 6e53e565fc6a
children f2843df56434
comparison
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9:6e53e565fc6a 10:df0c8d0a5992
1 <tool id="edger" name="edgeR" version="3.34.0+galaxy1"> 1 <tool id="edger" name="edgeR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description> 2 <description>
3 Perform differential expression of count data 3 Perform differential expression of count data
4 </description> 4 </description>
5 <macros>
6 <token name="@TOOL_VERSION@">3.34.0</token>
7 <token name="@VERSION_SUFFIX@">2</token>
8 </macros>
5 <xrefs> 9 <xrefs>
6 <xref type="bio.tools">edger</xref> 10 <xref type="bio.tools">edger</xref>
7 </xrefs> 11 </xrefs>
8 <edam_topics> 12 <edam_topics>
9 <edam_topic>topic_3308</edam_topic> 13 <edam_topic>topic_3308</edam_topic>
12 <edam_operation>operation_3563</edam_operation> 16 <edam_operation>operation_3563</edam_operation>
13 <edam_operation>operation_3223</edam_operation> 17 <edam_operation>operation_3223</edam_operation>
14 </edam_operations> 18 </edam_operations>
15 19
16 <requirements> 20 <requirements>
17 <requirement type="package" version="3.34.0">bioconductor-edger</requirement> 21 <requirement type="package" version="@TOOL_VERSION@">bioconductor-edger</requirement>
18 <requirement type="package" version="3.48.0">bioconductor-limma</requirement> 22 <requirement type="package" version="3.48.0">bioconductor-limma</requirement>
19 <requirement type="package" version="0.2.20">r-rjson</requirement> 23 <requirement type="package" version="0.2.20">r-rjson</requirement>
20 <requirement type="package" version="1.20.3">r-getopt</requirement> 24 <requirement type="package" version="1.20.3">r-getopt</requirement>
21 <requirement type="package" version="1.4.36">r-statmod</requirement> 25 <requirement type="package" version="1.4.36">r-statmod</requirement>
22 <!-- required for alpha function used with plotMD --> 26 <!-- required for alpha function used with plotMD -->
214 <conditional name="samples"> 218 <conditional name="samples">
215 <param name="count_select" type="select" label="Filter on Total Count or per Sample Count values?" > 219 <param name="count_select" type="select" label="Filter on Total Count or per Sample Count values?" >
216 <option value="total">Total</option> 220 <option value="total">Total</option>
217 <option value="sample">Sample</option> 221 <option value="sample">Sample</option>
218 </param> 222 </param>
219 <when value="total"> 223 <when value="total"/>
220 <param name="totReq" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Filter on Total Count" help="Apply the Minimum Count filter to genes after summing counts for all samples. See the Filter Low Counts section below for more information." />
221 </when>
222 <when value="sample"> 224 <when value="sample">
223 <param name="cntSampleReq" type="integer" value="0" min="0" label="Minimum Samples" 225 <param name="cntSampleReq" type="integer" value="0" min="0" label="Minimum Samples"
224 help="Filter out all genes that do not meet the Minimum Count in at least this many samples. See the Filter Low Counts section below for more information."/> 226 help="Filter out all genes that do not meet the Minimum Count in at least this many samples. See the Filter Low Counts section below for more information."/>
225 </when> 227 </when>
226 </conditional> 228 </conditional>