Mercurial > repos > iuc > limma_voom

comparison limma_voom.xml @ 26:119b069fc845 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit b4d788c0f159d507159117a063b1f867b243c738
author iuc
date Fri, 09 Feb 2024 17:06:25 +0000
parents d6f5fa4ee473
children
comparison
equal deleted inserted replaced
25:d6f5fa4ee473 26:119b069fc845
1 <tool id="limma_voom" name="limma" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="limma_voom" name="limma" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description> 2 <description>
3 Perform differential expression with limma-voom or limma-trend 3 Perform differential expression with limma-voom or limma-trend
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <token name="@TOOL_VERSION@">3.50.1</token> 6 <token name="@TOOL_VERSION@">3.58.1</token>
7 <token name="@VERSION_SUFFIX@">0</token>
8 <token name="@PROFILE@">23.0</token>
7 </macros> 9 </macros>
8 <xrefs>
9 <xref type="bio.tools">limma</xref>
10 </xrefs>
11 <edam_topics> 10 <edam_topics>
12 <edam_topic>topic_3308</edam_topic> 11 <edam_topic>topic_3308</edam_topic>
13 </edam_topics> 12 </edam_topics>
14 <edam_operations> 13 <edam_operations>
15 <edam_operation>operation_3563</edam_operation> 14 <edam_operation>operation_3563</edam_operation>
16 <edam_operation>operation_3223</edam_operation> 15 <edam_operation>operation_3223</edam_operation>
17 </edam_operations> 16 </edam_operations>
17 <xrefs>
18 <xref type="bio.tools">limma</xref>
19 <xref type="bioconductor">limma</xref>
20 </xrefs>
18 21
19 <requirements> 22 <requirements>
20 <requirement type="package" version="@TOOL_VERSION@">bioconductor-limma</requirement> 23 <requirement type="package" version="@TOOL_VERSION@">bioconductor-limma</requirement>
21 <requirement type="package" version="3.36.0">bioconductor-edger</requirement> 24 <requirement type="package" version="4.0.2">bioconductor-edger</requirement>
22 <requirement type="package" version="1.4.36">r-statmod</requirement> 25 <requirement type="package" version="1.5.0">r-statmod</requirement>
23 <requirement type="package" version="1.1.1">r-scales</requirement> 26 <requirement type="package" version="1.3.0">r-scales</requirement>
24 <requirement type="package" version="0.2.21">r-rjson</requirement> 27 <requirement type="package" version="0.2.21">r-rjson</requirement>
25 <requirement type="package" version="1.20.3">r-getopt</requirement> 28 <requirement type="package" version="1.20.4">r-getopt</requirement>
26 <requirement type="package" version="3.1.1">r-gplots</requirement> 29 <requirement type="package" version="3.1.3.1">r-gplots</requirement>
27 <requirement type="package" version="2.4.0">bioconductor-glimma</requirement> 30 <requirement type="package" version="2.12.0">bioconductor-glimma</requirement>
28 </requirements> 31 </requirements>
29 32
30 <version_command><![CDATA[ 33 <version_command><![CDATA[
31 echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", gplots version" $(R --vanilla --slave -e "library(gplots); cat(sessionInfo()\$otherPkgs\$gplots\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", Glimma version" $(R --vanilla --slave -e "library(Glimma); cat(sessionInfo()\$otherPkgs\$Glimma\$Version)" 2> /dev/null | grep -v -i "WARNING: ") 34 echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", gplots version" $(R --vanilla --slave -e "library(gplots); cat(sessionInfo()\$otherPkgs\$gplots\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", Glimma version" $(R --vanilla --slave -e "library(Glimma); cat(sessionInfo()\$otherPkgs\$Glimma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
32 ]]></version_command> 35 ]]></version_command>
731 <param name="cfile" value="yes" /> 734 <param name="cfile" value="yes" />
732 <param name="cinfo" value="contrasts.txt" ftype="tabular" /> 735 <param name="cinfo" value="contrasts.txt" ftype="tabular" />
733 <param name="normalisationOption" value="TMM" /> 736 <param name="normalisationOption" value="TMM" />
734 <param name="topgenes" value="6" /> 737 <param name="topgenes" value="6" />
735 <output_collection name="outTables" count="3"> 738 <output_collection name="outTables" count="3">
739 <element name="limma-voom_Mut-WT-WT-Mut" ftype="tabular" >
740 <assert_contents>
741 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
742 <has_text_matching expression="11304.*0.9146" />
743 </assert_contents>
744 </element>
736 <element name="limma-voom_Mut-WT" ftype="tabular" > 745 <element name="limma-voom_Mut-WT" ftype="tabular" >
737 <assert_contents> 746 <assert_contents>
738 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" /> 747 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
739 <has_text_matching expression="11304.*0.4573" /> 748 <has_text_matching expression="11304.*0.4573" />
740 </assert_contents> 749 </assert_contents>
741 </element> 750 </element>
742 <element name="limma-voom_WT-Mut" ftype="tabular" > 751 <element name="limma-voom_WT-Mut" ftype="tabular" >
743 <assert_contents> 752 <assert_contents>
744 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" /> 753 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
745 <has_text_matching expression="11304.*-0.4573" /> 754 <has_text_matching expression="11304.*-0.4573" />
746 </assert_contents>
747 </element>
748 <element name="limma-voom_Mut-WT-WT-Mut" ftype="tabular" >
749 <assert_contents>
750 <has_text_matching expression="GeneID.*logFC.*AveExpr.*t.*P.Value.*adj.P.Val.*B" />
751 <has_text_matching expression="11304.*0.9146" />
752 </assert_contents> 755 </assert_contents>
753 </element> 756 </element>
754 </output_collection> 757 </output_collection>
755 </test> 758 </test>
756 </tests> 759 </tests>