edger: edger.xml annotate

annotate edger.xml @ 16:09965c918573 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 96699cdbdadf0a1c40fdbd87f870b47049c0449f

author	iuc
date	Wed, 15 Oct 2025 12:56:21 +0000
parents	119f41ec0ada
children

rev	line source
10 acc76f69e8cc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 38cf93fd693c810b4150c5d8aa3763aebc988b07" iuc parents: 9 diff changeset	1 <tool id="edger" name="edgeR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	2 <description>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	3 Perform differential expression of count data
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	4 </description>
10 acc76f69e8cc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 38cf93fd693c810b4150c5d8aa3763aebc988b07" iuc parents: 9 diff changeset	5 <macros>
11 f034bbfb7062 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 23907b040426238b00ca0644a643c3ff0b3451b9" iuc parents: 10 diff changeset	6 <token name="@TOOL_VERSION@">3.36.0</token>
16 09965c918573 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 96699cdbdadf0a1c40fdbd87f870b47049c0449f iuc parents: 15 diff changeset	7 <token name="@VERSION_SUFFIX@">7</token>
10 acc76f69e8cc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 38cf93fd693c810b4150c5d8aa3763aebc988b07" iuc parents: 9 diff changeset	8 </macros>
8 ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 7 diff changeset	9 <edam_topics>
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 7 diff changeset	10 <edam_topic>topic_3308</edam_topic>
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 7 diff changeset	11 </edam_topics>
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 7 diff changeset	12 <edam_operations>
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 7 diff changeset	13 <edam_operation>operation_3563</edam_operation>
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 7 diff changeset	14 <edam_operation>operation_3223</edam_operation>
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 7 diff changeset	15 </edam_operations>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	16 <xrefs>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	17 <xref type="bio.tools">edger</xref>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	18 <xref type="bioconductor">edger</xref>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	19 </xrefs>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	20 <requirements>
10 acc76f69e8cc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 38cf93fd693c810b4150c5d8aa3763aebc988b07" iuc parents: 9 diff changeset	21 <requirement type="package" version="@TOOL_VERSION@">bioconductor-edger</requirement>
11 f034bbfb7062 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 23907b040426238b00ca0644a643c3ff0b3451b9" iuc parents: 10 diff changeset	22 <requirement type="package" version="3.50.0">bioconductor-limma</requirement>
4 9a62dbdb122b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	23 <requirement type="package" version="0.2.20">r-rjson</requirement>
8 ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 7 diff changeset	24 <requirement type="package" version="1.20.3">r-getopt</requirement>
ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 7 diff changeset	25 <requirement type="package" version="1.4.36">r-statmod</requirement>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	26 <!-- required for alpha function used with plotMD -->
8 ea85027d986c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 7 diff changeset	27 <requirement type="package" version="1.1.1">r-scales</requirement>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	28 </requirements>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	29 <version_command><![CDATA[
2 3de72f1f78aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	30 echo $(R --version \| grep version \| grep -v GNU)", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null \| grep -v -i "WARNING: ")", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$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" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null \| grep -v -i "WARNING: ")
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	31 ]]></version_command>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	32 <command detect_errors="exit_code"><![CDATA[
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	33 #import json
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	34 Rscript '$__tool_directory__/edger.R'
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	35
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	36 -R '$outReport'
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	37 -o '$outReport.files_path'
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	38
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	39 #if $input.format=="files":
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	40
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	41 ## Adapted from DESeq2 wrapper
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	42 #set $temp_factor_names = list()
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	43 #for $fact in $input.rep_factor:
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	44 #set $temp_factor = list()
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	45 #for $g in $fact.rep_group:
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	46 #set $count_files = list()
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	47 #for $file in $g.countsFile:
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	48 $count_files.append(str($file))
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	49 #end for
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	50 $temp_factor.append( {str($g.groupName): $count_files} )
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	51 #end for
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	52
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	53 $temp_factor.reverse()
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	54 $temp_factor_names.append([str($fact.factorName), $temp_factor])
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	55 #end for
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	56 -j '#echo json.dumps(temp_factor_names)#'
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	57
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	58 #elif $input.format=="matrix":
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	59 -m '$input.counts'
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	60 #if $input.fact.ffile=='yes':
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	61 -f '$input.fact.finfo'
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	62 #else:
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	63 -i '${ '\|'.join( ['%s::%s' % ($x.factorName, $x.groupNames) for x in $input.fact.rep_factor] ) }'
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	64 #end if
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	65 #end if
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	66
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	67 #if $anno.annoOpt=='yes':
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	68 -a '$anno.geneanno'
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	69 #end if
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	70
14 c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	71 #if $formula:
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	72 -F '$formula'
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	73 #end if
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	74
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	75 #if $contrasts.contrastOpt == 'file':
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	76 -C '$contrasts.cinfo'
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	77 #else:
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	78 -C '${ ','.join( ['%s' % $x.contrast for x in $contrasts.rep_contrast] ) }'
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	79 #end if
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	80
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	81 #if $f.filt.filt_select == 'yes':
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	82 #if $f.filt.cformat.format_select == 'cpm':
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	83 -c '$f.filt.cformat.cpmReq'
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	84 -s '$f.filt.cformat.cpmSampleReq'
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	85 #elif $f.filt.cformat.format_select == 'counts':
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	86 -z '$f.filt.cformat.cntReq'
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	87 #if $f.filt.cformat.samples.count_select == 'total':
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	88 -y
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	89 #elif $f.filt.cformat.samples.count_select == 'sample':
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	90 -s '$f.filt.cformat.samples.cntSampleReq'
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	91 #end if
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	92 #end if
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	93 #end if
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	94
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	95 #if $out.normCounts:
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	96 -x
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	97 #end if
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	98 #if $out.rdaOption:
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	99 -r
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	100 #end if
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	101
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	102 -l '$adv.lfc'
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	103 -p '$adv.pVal'
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	104 -d '$adv.pAdjust'
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	105 -n '$adv.normalisationOption'
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	106 #if $adv.robOption:
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	107 -b
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	108 #end if
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	109 #if $adv.lrtOption:
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	110 -t
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	111 #end if
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	112
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	113 &&
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	114 mkdir ./output_dir
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	115
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	116 &&
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	117 cp '$outReport.files_path'/*.tsv output_dir/
2 3de72f1f78aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	118
3de72f1f78aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	119 #if $out.rscript:
3de72f1f78aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	120 && cp '$__tool_directory__/edger.R' '$rscript'
3de72f1f78aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	121 #end if
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	122 ]]></command>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	123 <inputs>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	124 <!-- Counts and Factors -->
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	125 <conditional name="input">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	126 <param name="format" type="select" label="Count Files or Matrix?" help="You can choose to input either separate count files (one per sample) or a single count matrix">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	127 <option value="files">Separate Count Files</option>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	128 <option value="matrix">Single Count Matrix</option>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	129 </param>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	130 <when value="files">
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	131 <repeat name="rep_factor" title="Factor" min="1">
6 7cf6248bc173 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 21f0bc6c64129122212a6d182fdf3e360617e629 iuc parents: 5 diff changeset	132 <param name="factorName" type="text" label="Name" help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Optional additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section for more information. NOTE: Please only use letters, numbers or underscores, and the first character of each factor must be a letter">
14 c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	133 <validator type="empty_field"/>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	134 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	135 </param>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	136 <repeat name="rep_group" title="Group" min="2" default="2">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	137 <param name="groupName" type="text" label="Name" help="Name of group that the counts files belong to (e.g. WT or Mut). NOTE: Please only use letters, numbers or underscores (case sensitive), and the first character of each group must be a letter">
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	138 <sanitizer>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	139 <valid initial="string.letters,string.digits">
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	140 <add value="_"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	141 </valid>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	142 </sanitizer>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	143 </param>
3 2aa9dd87aad3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	144 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts files"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	145 </repeat>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	146 </repeat>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	147 </when>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	148 <when value="matrix">
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	149 <param name="counts" type="data" format="tabular" label="Count Matrix"/>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	150 <conditional name="fact">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	151 <param name="ffile" type="select" label="Input factor information from file?" help="You can choose to input the factor and group information for the samples from a file or manually enter below. NOTE: Please only use letters, numbers or underscores (case sensitive), and the first character of each sample, factor and group must be a letter">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	152 <option value="no">No</option>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	153 <option value="yes">Yes</option>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	154 </param>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	155 <when value="yes">
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	156 <param name="finfo" type="data" format="tabular" label="Factor File"/>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	157 </when>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	158 <when value="no">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	159 <repeat name="rep_factor" title="Factor" min="1">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	160 <param name="factorName" type="text" label="Factor Name" help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section below. NOTE: Please only use letters, numbers or underscores, and the first character of each factor must be a letter">
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	161 <validator type="empty_field"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	162 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	163 </param>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	164 <param name="groupNames" type="text" label="Groups" help="Enter the group names for the samples separated with commas e.g. WT,WT,WT,Mut,Mut,Mut. The order of the names must match the order of the samples in the columns of the count matrix. NOTE: Please only use letters, numbers or underscores (case sensitive), and the first character of each group must be a letter">
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	165 <validator type="empty_field"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	166 <validator type="regex" message="Please only use letters, numbers or underscores, and separate levels by commas">^[\w,]+$</validator>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	167 </param>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	168 </repeat>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	169 </when>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	170 </conditional>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	171 </when>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	172 </conditional>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	173 <!-- Gene Annotations -->
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	174 <conditional name="anno">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	175 <param name="annoOpt" type="select" label="Use Gene Annotations?" help="If you provide an annotation file, annotations will be added to the table(s) of differential expression results to provide descriptions for each gene. See Help section below.">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	176 <option value="no">No</option>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	177 <option value="yes">Yes</option>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	178 </param>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	179 <when value="yes">
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	180 <param name="geneanno" type="data" format="tabular" label="Gene Annotations"/>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	181 </when>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	182 <when value="no"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	183 </conditional>
14 c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	184 <!-- Optional formula -->
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	185 <param name="formula" type="text" optional="true" label="Formula for linear model" help="An optional formula for the EdgeR linear model, this will override the use of the fields in factors as a simple sum. The formula can only use elements available in the factors file. This needs to be exactly as EdgeR expect the formula, ie. `~ 0 + factor_A + factor_B:factor_C`. See EdgeR documentation for more details.">
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	186 <sanitizer invalid_char="">
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	187 <valid initial="string.letters,string.digits">
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	188 <add value="_"/>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	189 <add value="-"/>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	190 <add value="+"/>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	191 <add value="*"/>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	192 <add value="/"/>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	193 <add value="^"/>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	194 <add value=":"/>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	195 <add value="."/>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	196 <add value="~"/>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	197 <add value=" "/>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	198 <add value="("/>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	199 <add value=")"/>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	200 <add value="@"/>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	201 <add value="$"/>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	202 </valid>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	203 </sanitizer>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	204 </param>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	205 <!-- Contrasts -->
14 c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	206 <conditional name="contrasts">
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	207 <param name="contrastOpt" type="select" label="Input contrasts manually or through a file">
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	208 <option value="manual">manually</option>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	209 <option value="file">file</option>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	210 </param>
14 c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	211 <when value="manual">
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	212 <repeat name="rep_contrast" title="Contrast" min="1" default="1">
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	213 <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For differences between contrasts use e.g. (MT.t1-MT.t0)-(WT.t1-WT.t0). For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf or https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf page 36 for nested comparisons.">
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	214 <validator type="empty_field"/>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	215 <validator type="regex" message="Please only use letters, numbers, parentheses, colon or underscores">^[\w\-():]+$</validator>
14 c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	216 </param>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	217 </repeat>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	218 </when>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	219 <when value="file">
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	220 <param name="cinfo" optional="true" type="data" format="tabular" label="Contrasts File" help="Setting this file will ignore any manually added contrasts above, make sure to remove any contrast fields above pressing the trash bin icon, or the tool will fail. First line of the file must be a header, below that each separate contrast should be on a line. Contrast formulas need to be based on ther factors data and potentially the formula provided. See EdgeR documentation on contrasts for more details."/>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	221 </when>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	222 </conditional>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	223 <!-- Filter Options -->
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	224 <section name="f" expanded="false" title="Filter Low Counts">
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	225 <conditional name="filt">
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	226 <param name="filt_select" type="select" label="Filter lowly expressed genes?" help="Treat genes with very low expression as unexpressed and filter out. See the Filter Low Counts section below for more information. Default: No">
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	227 <option value="no" selected="true">No</option>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	228 <option value="yes">Yes</option>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	229 </param>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	230 <when value="yes">
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	231 <conditional name="cformat">
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	232 <param name="format_select" type="select" label="Filter on CPM or Count values?" help="It is slightly better to base the filtering on count-per-million (CPM) rather than the raw count values so as to avoid favoring genes expressed in samples sequenced to a higher depth. ">
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	233 <option value="cpm">CPM</option>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	234 <option value="counts">Counts</option>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	235 </param>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	236 <when value="cpm">
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	237 <param name="cpmReq" type="float" value="1" min="0" label="Minimum CPM" help="Treat genes with CPM below this value as unexpressed and filter out. See the Filter Low Counts section below for more information."/>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	238 <param name="cpmSampleReq" type="integer" value="0" min="0" label="Minimum Samples" help="Filter out all genes that do not meet the Minimum CPM in at least this many samples. See the Filter Low Counts section below for more information."/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	239 </when>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	240 <when value="counts">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	241 <param name="cntReq" type="integer" value="0" min="0" label="Minimum Count" help="Filter out all genes that do not meet this minimum count. You can choose below to apply this filter to the total count for all samples or specify the number of samples under Minimum Samples. See the Filter Low Counts section below for more information."/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	242 <conditional name="samples">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	243 <param name="count_select" type="select" label="Filter on Total Count or per Sample Count values?">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	244 <option value="total">Total</option>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	245 <option value="sample">Sample</option>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	246 </param>
10 acc76f69e8cc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 38cf93fd693c810b4150c5d8aa3763aebc988b07" iuc parents: 9 diff changeset	247 <when value="total"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	248 <when value="sample">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	249 <param name="cntSampleReq" type="integer" value="0" min="0" label="Minimum Samples" 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."/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	250 </when>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	251 </conditional>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	252 </when>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	253 </conditional>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	254 </when>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	255 <when value="no"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	256 </conditional>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	257 </section>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	258 <!-- Output Options -->
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	259 <section name="out" expanded="false" title="Output Options">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	260 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Output Normalised Counts Table?" help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	261 </param>
2 3de72f1f78aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	262 <param name="rscript" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used will be provided as a text file in the output. Default: No"/>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	263 <param name="rdaOption" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Output RData file?" help="Output all the data used by R to construct the plots and tables, can be loaded into R. A link to the RData file will be provided in the HTML report. Default: No">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	264 </param>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	265 </section>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	266 <!-- Advanced Options -->
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	267 <section name="adv" expanded="false" title="Advanced Options">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	268 <param name="lfc" type="float" value="0" min="0" label="Minimum Log2 Fold Change" help="Genes above this threshold and below the p-value threshold are considered significant and highlighted in the MD plot. Default: 0."/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	269 <param name="pVal" type="float" value="0.05" min="0" max="1" label="P-Value Adjusted Threshold" help="Genes below this threshold are considered significant and highlighted in the MD plot. If either BH(1995) or BY(2001) are selected then this value is a false-discovery-rate control. If Holm(1979) is selected then this is an adjusted p-value for family-wise error rate. Default: 0.05."/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	270 <param name="pAdjust" type="select" label="P-Value Adjustment Method" help="Default: BH">
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	271 <option value="BH" selected="true">Benjamini and Hochberg (1995)</option>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	272 <option value="BY">Benjamini and Yekutieli (2001)</option>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	273 <option value="holm">Holm (1979)</option>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	274 <option value="none">None</option>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	275 </param>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	276 <param name="normalisationOption" type="select" label="Normalisation Method" help="Default: TMM">
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	277 <option value="TMM" selected="true">TMM</option>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	278 <option value="RLE">RLE</option>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	279 <option value="upperquartile">Upperquartile</option>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	280 <option value="none">None (Don't normalise)</option>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	281 </param>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	282 <param name="robOption" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use Robust Settings?" help="Using robust settings is usually recommended to protect against outlier genes. Default: Yes"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	283 <param name="lrtOption" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use Likelihood Ratio Test?" help="Use likelihood ratio test instead of quasi-likelihood F-test. Default: No"/>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	284 </section>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	285 </inputs>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	286 <outputs>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	287 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	288 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: Tables">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	289 <discover_datasets pattern="(?P<name>.+)\.tsv$" format="tabular" directory="output_dir" visible="false"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	290 </collection>
2 3de72f1f78aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	291 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript">
3de72f1f78aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	292 <filter>out['rscript']</filter>
3de72f1f78aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	293 </data>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	294 </outputs>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	295 <tests>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	296 <!-- Ensure report is output -->
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	297 <test expect_num_outputs="2">
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	298 <param name="input\|format" value="matrix"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	299 <param name="input\|counts" value="matrix.txt"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	300 <param name="input\|fact\|ffile" value="no"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	301 <repeat name="input\|fact\|rep_factor">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	302 <param name="factorName" value="Genotype"/>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	303 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	304 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	305 <param name="contrasts\|contrastOpt" value="manual"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	306 <repeat name="contrasts\|rep_contrast">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	307 <param name="contrast" value="Mut-WT"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	308 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	309 <repeat name="contrasts\|rep_contrast">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	310 <param name="contrast" value="WT-Mut"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	311 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	312 <param name="adv\|normalisationOption" value="TMM"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	313 <output_collection name="outTables" count="2">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	314 <element name="edgeR_Mut-WT" ftype="tabular">
2 3de72f1f78aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	315 <assert_contents>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	316 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	317 <has_text_matching expression="11304.*0.4582"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	318 </assert_contents>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	319 </element>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	320 <element name="edgeR_WT-Mut" ftype="tabular">
2 3de72f1f78aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	321 <assert_contents>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	322 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	323 <has_text_matching expression="11304.*-0.4582"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	324 </assert_contents>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	325 </element>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	326 </output_collection>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	327 <output name="outReport">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	328 <assert_contents>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	329 <has_text text="edgeR Analysis Output"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	330 <has_text text="quasi-likelihood"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	331 <not_has_text text="likelihood ratio"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	332 <not_has_text text="RData"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	333 </assert_contents>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	334 </output>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	335 </test>
7 47094543a5ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	336 <!-- Complex contrasts constructions -->
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	337 <test expect_num_outputs="2">
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	338 <param name="input\|format" value="matrix"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	339 <param name="input\|counts" value="matrix-complex.txt"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	340 <param name="input\|fact\|ffile" value="no"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	341 <repeat name="input\|fact\|rep_factor">
7 47094543a5ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	342 <param name="factorName" value="Genotype"/>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	343 <param name="groupNames" value="MutA,MutA,MutA,MutB,MutB,MutB,WTA,WTA,WTA,WTB,WTB,WTB"/>
7 47094543a5ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	344 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	345 <param name="contrasts\|contrastOpt" value="manual"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	346 <repeat name="contrasts\|rep_contrast">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	347 <param name="contrast" value="(MutA-MutB)-(WTA-WTB)"/>
7 47094543a5ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	348 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	349 <param name="adv\|normalisationOption" value="TMM"/>
7 47094543a5ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	350 <output_collection name="outTables" count="1">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	351 <element name="edgeR_(MutA-MutB)-(WTA-WTB)" ftype="tabular">
7 47094543a5ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	352 <assert_contents>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	353 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	354 <has_text_matching expression="11304.*15.53"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	355 </assert_contents>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	356 </element>
7 47094543a5ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	357 </output_collection>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	358 <output name="outReport">
7 47094543a5ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	359 <assert_contents>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	360 <has_text text="edgeR Analysis Output"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	361 <has_text text="quasi-likelihood"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	362 <not_has_text text="likelihood ratio"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	363 <not_has_text text="RData"/>
7 47094543a5ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	364 </assert_contents>
47094543a5ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	365 </output>
47094543a5ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	366 </test>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	367 <!-- Ensure annotation file input works -->
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	368 <test expect_num_outputs="2">
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	369 <param name="input\|format" value="matrix"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	370 <param name="anno\|annoOpt" value="yes"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	371 <param name="anno\|geneanno" value="anno.txt"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	372 <param name="input\|counts" value="matrix.txt"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	373 <param name="input\|fact\|ffile" value="no"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	374 <repeat name="input\|fact\|rep_factor">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	375 <param name="factorName" value="Genotype"/>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	376 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	377 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	378 <param name="contrasts\|contrastOpt" value="manual"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	379 <repeat name="contrasts\|rep_contrast">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	380 <param name="contrast" value="Mut-WT"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	381 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	382 <param name="adv\|normalisationOption" value="TMM"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	383 <output_collection name="outTables" count="1">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	384 <element name="edgeR_Mut-WT" ftype="tabular">
2 3de72f1f78aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	385 <assert_contents>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	386 <has_text_matching expression="EntrezID.Symbol.logFC.logCPM.F.PValue.FDR"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	387 <has_text_matching expression="11304.Abca4.0.4582"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	388 </assert_contents>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	389 </element>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	390 </output_collection>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	391 </test>
2 3de72f1f78aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	392 <!-- Ensure RScript and RData file can be output -->
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	393 <test expect_num_outputs="3">
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	394 <param name="input\|format" value="matrix"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	395 <param name="out\|rscript" value="True"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	396 <param name="out\|rdaOption" value="true"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	397 <param name="input\|counts" value="matrix.txt"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	398 <param name="input\|fact\|ffile" value="no"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	399 <repeat name="input\|fact\|rep_factor">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	400 <param name="factorName" value="Genotype"/>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	401 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	402 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	403 <param name="contrasts\|contrastOpt" value="manual"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	404 <repeat name="contrasts\|rep_contrast">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	405 <param name="contrast" value="Mut-WT"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	406 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	407 <param name="adv\|normalisationOption" value="TMM"/>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	408 <output name="outReport">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	409 <assert_contents>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	410 <has_text text="RData"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	411 </assert_contents>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	412 </output>
4 9a62dbdb122b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	413 <output name="rscript">
9a62dbdb122b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	414 <assert_contents>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	415 <has_text_matching expression="Task run time"/>
4 9a62dbdb122b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	416 </assert_contents>
9a62dbdb122b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	417 </output>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	418 </test>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	419 <!-- Ensure secondary factors work -->
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	420 <test expect_num_outputs="2">
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	421 <param name="input\|format" value="matrix"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	422 <param name="input\|counts" value="matrix.txt"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	423 <param name="input\|fact\|ffile" value="no"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	424 <repeat name="input\|fact\|rep_factor">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	425 <param name="factorName" value="Genotype"/>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	426 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	427 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	428 <repeat name="input\|fact\|rep_factor">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	429 <param name="factorName" value="Batch"/>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	430 <param name="groupNames" value="b1,b2,b3,b1,b2,b3"/>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	431 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	432 <param name="contrasts\|contrastOpt" value="manual"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	433 <repeat name="contrasts\|rep_contrast">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	434 <param name="contrast" value="Mut-WT"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	435 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	436 <param name="adv\|normalisationOption" value="TMM"/>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	437 <output_collection name="outTables" count="1">
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	438 <element name="edgeR_Mut-WT" ftype="tabular">
2 3de72f1f78aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	439 <assert_contents>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	440 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	441 <has_text_matching expression="11304.*0.4584"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	442 </assert_contents>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	443 </element>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	444 </output_collection>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	445 </test>
4 9a62dbdb122b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	446 <!-- Ensure factors file with unordered samples works -->
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	447 <test expect_num_outputs="2">
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	448 <param name="input\|format" value="matrix"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	449 <param name="input\|fact\|ffile" value="yes"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	450 <param name="input\|fact\|finfo" value="factorinfo.txt"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	451 <param name="input\|counts" value="matrix.txt"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	452 <param name="contrasts\|contrastOpt" value="manual"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	453 <repeat name="contrasts\|rep_contrast">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	454 <param name="contrast" value="Mut-WT"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	455 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	456 <param name="adv\|normalisationOption" value="TMM"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	457 <output_collection name="outTables" count="1">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	458 <element name="edgeR_Mut-WT" ftype="tabular">
2 3de72f1f78aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	459 <assert_contents>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	460 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	461 <has_text_matching expression="11304.*0.4584"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	462 </assert_contents>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	463 </element>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	464 </output_collection>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	465 </test>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	466 <!-- Ensure normalised counts file output works-->
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	467 <test expect_num_outputs="2">
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	468 <param name="input\|format" value="matrix"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	469 <param name="out\|normCounts" value="true"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	470 <param name="input\|counts" value="matrix.txt"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	471 <param name="input\|fact\|ffile" value="no"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	472 <repeat name="input\|fact\|rep_factor">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	473 <param name="factorName" value="Genotype"/>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	474 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	475 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	476 <param name="contrasts\|contrastOpt" value="manual"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	477 <repeat name="contrasts\|rep_contrast">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	478 <param name="contrast" value="Mut-WT"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	479 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	480 <param name="adv\|normalisationOption" value="TMM"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	481 <output_collection name="outTables" count="2">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	482 <element name="edgeR_Mut-WT" ftype="tabular">
2 3de72f1f78aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	483 <assert_contents>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	484 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	485 <has_text_matching expression="11304.*0.4582"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	486 </assert_contents>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	487 </element>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	488 <element name="edgeR_normcounts" ftype="tabular">
2 3de72f1f78aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	489 <assert_contents>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	490 <has_text_matching expression="GeneID.Mut1.Mut2.Mut3.WT1.WT2.WT3"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	491 <has_text_matching expression="11304.*15.75"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	492 </assert_contents>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	493 </element>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	494 </output_collection>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	495 </test>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	496 <!-- Ensure likelihood ratio option works -->
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	497 <test expect_num_outputs="2">
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	498 <param name="input\|format" value="matrix"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	499 <param name="input\|counts" value="matrix.txt"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	500 <param name="input\|fact\|ffile" value="no"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	501 <repeat name="input\|fact\|rep_factor">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	502 <param name="factorName" value="Genotype"/>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	503 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	504 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	505 <param name="contrasts\|contrastOpt" value="manual"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	506 <repeat name="contrasts\|rep_contrast">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	507 <param name="contrast" value="Mut-WT"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	508 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	509 <param name="adv\|normalisationOption" value="TMM"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	510 <param name="adv\|lrtOption" value="true"/>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	511 <output name="outReport">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	512 <assert_contents>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	513 <has_text text="likelihood ratio"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	514 <not_has_text text="quasi-likelihood"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	515 </assert_contents>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	516 </output>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	517 </test>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	518 <!-- Ensure multiple counts files input works -->
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	519 <test expect_num_outputs="2">
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	520 <param name="input\|format" value="files"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	521 <repeat name="input\|rep_factor">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	522 <param name="factorName" value="Genotype"/>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	523 <repeat name="rep_group">
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	524 <param name="groupName" value="WT"/>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	525 <param name="countsFile" value="WT1.counts,WT2.counts,WT3.counts"/>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	526 </repeat>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	527 <repeat name="rep_group">
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	528 <param name="groupName" value="Mut"/>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	529 <param name="countsFile" value="Mut1.counts,Mut2.counts,Mut3.counts"/>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	530 </repeat>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	531 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	532 <repeat name="input\|rep_factor">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	533 <param name="factorName" value="Batch"/>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	534 <repeat name="rep_group">
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	535 <param name="groupName" value="b1"/>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	536 <param name="countsFile" value="WT1.counts,Mut1.counts"/>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	537 </repeat>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	538 <repeat name="rep_group">
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	539 <param name="groupName" value="b2"/>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	540 <param name="countsFile" value="WT2.counts,Mut2.counts"/>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	541 </repeat>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	542 <repeat name="rep_group">
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	543 <param name="groupName" value="b3"/>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	544 <param name="countsFile" value="WT3.counts,Mut3.counts"/>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	545 </repeat>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	546 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	547 <param name="anno\|annoOpt" value="yes"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	548 <param name="anno\|geneanno" value="anno.txt"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	549 <param name="contrasts\|contrastOpt" value="manual"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	550 <repeat name="contrasts\|rep_contrast">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	551 <param name="contrast" value="Mut-WT"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	552 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	553 <repeat name="contrasts\|rep_contrast">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	554 <param name="contrast" value="WT-Mut"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	555 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	556 <param name="out\|normCounts" value="true"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	557 <output_collection name="outTables" count="3">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	558 <element name="edgeR_Mut-WT" ftype="tabular">
2 3de72f1f78aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	559 <assert_contents>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	560 <has_text_matching expression="EntrezID.Symbol.logFC.logCPM.F.PValue.FDR"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	561 <has_text_matching expression="11304.Abca4.0.4584"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	562 </assert_contents>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	563 </element>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	564 <element name="edgeR_WT-Mut" ftype="tabular">
2 3de72f1f78aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	565 <assert_contents>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	566 <has_text_matching expression="logFC.logCPM.F.PValue.FDR"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	567 <has_text_matching expression="11304.Abca4.-0.4584"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	568 </assert_contents>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	569 </element>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	570 <element name="edgeR_normcounts" ftype="tabular">
2 3de72f1f78aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	571 <assert_contents>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	572 <has_text_matching expression="Mut1.Mut2.Mut3.WT1.WT2.*WT3"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	573 <has_text_matching expression="11304.Abca4.15.75"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	574 </assert_contents>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	575 </element>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	576 </output_collection>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	577 </test>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	578 <!-- Ensure filtering on CPM in Mnimum Samples works -->
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	579 <test expect_num_outputs="2">
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	580 <param name="input\|format" value="matrix"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	581 <param name="input\|counts" value="matrix.txt"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	582 <param name="input\|fact\|ffile" value="no"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	583 <repeat name="input\|fact\|rep_factor">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	584 <param name="factorName" value="Genotype"/>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	585 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	586 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	587 <param name="contrasts\|contrastOpt" value="manual"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	588 <repeat name="contrasts\|rep_contrast">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	589 <param name="contrast" value="Mut-WT"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	590 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	591 <param name="adv\|normalisationOption" value="TMM"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	592 <param name="f\|filt\|filt_select" value="yes"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	593 <param name="f\|filt\|cformat\|format_select" value="cpm"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	594 <!-- real cpmReq values would be a lot lower
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	595 this is just for this tiny test dataset -->
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	596 <param name="f\|filt\|cformat\|cpmReq" value="1000"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	597 <param name="f\|filt\|cformat\|cpmSampleReq" value="3"/>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	598 <output name="outReport">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	599 <assert_contents>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	600 <has_text text="CPM in at least"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	601 <not_has_text text="after summing counts for all samples"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	602 <not_has_text text="counts in at least"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	603 </assert_contents>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	604 </output>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	605 <output_collection name="outTables" count="1">
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	606 <element name="edgeR_Mut-WT" ftype="tabular">
2 3de72f1f78aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	607 <assert_contents>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	608 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	609 <has_text_matching expression="11304.*0.4568"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	610 <not_has_text text="-0.0682"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	611 </assert_contents>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	612 </element>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	613 </output_collection>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	614 </test>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	615 <!-- Ensure filtering on Count in Minmum Samples works -->
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	616 <test expect_num_outputs="2">
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	617 <param name="input\|format" value="matrix"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	618 <param name="input\|counts" value="matrix.txt"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	619 <param name="input\|fact\|ffile" value="no"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	620 <repeat name="input\|fact\|rep_factor">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	621 <param name="factorName" value="Genotype"/>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	622 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	623 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	624 <param name="contrasts\|contrastOpt" value="manual"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	625 <repeat name="contrasts\|rep_contrast">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	626 <param name="contrast" value="Mut-WT"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	627 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	628 <param name="adv\|normalisationOption" value="TMM"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	629 <param name="f\|filt\|filt_select" value="yes"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	630 <param name="f\|filt\|cformat\|format_select" value="counts"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	631 <param name="f\|filt\|cformat\|cntReq" value="10"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	632 <param name="f\|filt\|cformat\|samples\|count_select" value="sample"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	633 <param name="f\|filt\|cformat\|samples\|cntSampleReq" value="3"/>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	634 <output name="outReport">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	635 <assert_contents>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	636 <has_text text="counts in at least"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	637 <not_has_text text="after summing counts for all samples"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	638 <not_has_text text="CPM in at least"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	639 </assert_contents>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	640 </output>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	641 <output_collection name="outTables" count="1">
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	642 <element name="edgeR_Mut-WT" ftype="tabular">
2 3de72f1f78aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	643 <assert_contents>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	644 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	645 <has_text_matching expression="11304.*0.4568"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	646 <not_has_text text="-0.0682"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	647 </assert_contents>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	648 </element>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	649 </output_collection>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	650 </test>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	651 <!-- Ensure filtering on Total Count works -->
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	652 <test expect_num_outputs="2">
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	653 <param name="input\|format" value="matrix"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	654 <param name="input\|counts" value="matrix.txt"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	655 <param name="input\|fact\|ffile" value="no"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	656 <repeat name="input\|fact\|rep_factor">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	657 <param name="factorName" value="Genotype"/>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	658 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	659 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	660 <param name="contrasts\|contrastOpt" value="manual"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	661 <repeat name="contrasts\|rep_contrast">
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	662 <param name="contrast" value="Mut-WT"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	663 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	664 <param name="adv\|normalisationOption" value="TMM"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	665 <param name="f\|filt\|filt_select" value="yes"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	666 <param name="f\|filt\|cformat\|format_select" value="counts"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	667 <!-- real cntReq values would be a lot lower
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	668 this is just for this tiny test dataset -->
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	669 <param name="f\|filt\|cformat\|cntReq" value="1000"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	670 <param name="f\|filt\|cformat\|samples\|count_select" value="total"/>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	671 <output name="outReport">
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	672 <assert_contents>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	673 <has_text text="after summing counts for all samples"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	674 <not_has_text text="counts in at least"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	675 <not_has_text text="CPM in at least"/>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	676 </assert_contents>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	677 </output>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	678 <output_collection name="outTables" count="1">
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	679 <element name="edgeR_Mut-WT" ftype="tabular">
2 3de72f1f78aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	680 <assert_contents>
12 07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	681 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	682 <has_text_matching expression="11304.*0.4568"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	683 <not_has_text text="-0.0682"/>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	684 </assert_contents>
07cc368bf34f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc iuc parents: 11 diff changeset	685 </element>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	686 </output_collection>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	687 </test>
14 c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	688 <!-- Ensure formula and contrast file work -->
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	689 <test expect_num_outputs="2">
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	690 <param name="input\|format" value="matrix"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	691 <param name="input\|counts" value="matrix.txt"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	692 <param name="input\|fact\|ffile" value="no"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	693 <repeat name="input\|fact\|rep_factor">
14 c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	694 <param name="factorName" value="Genotype"/>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	695 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT"/>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	696 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	697 <repeat name="input\|fact\|rep_factor">
14 c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	698 <param name="factorName" value="Batch"/>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	699 <param name="groupNames" value="b1,b2,b3,b1,b2,b3"/>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	700 </repeat>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	701 <param name="contrasts\|contrastOpt" value="file"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	702 <param name="contrasts\|cinfo" value="contrasts_file.txt"/>
14 c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	703 <param name="formula" value="~ 0 + Genotype + Batch"/>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	704 <param name="adv\|normalisationOption" value="TMM"/>
14 c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	705 <output_collection name="outTables" count="3">
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	706 <element name="edgeR_Mut-WT" ftype="tabular">
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	707 <assert_contents>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	708 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR"/>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	709 <has_text_matching expression="11304.*0.4584"/>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	710 </assert_contents>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	711 </element>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	712 <element name="edgeR_WT-Mut" ftype="tabular">
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	713 <assert_contents>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	714 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR"/>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	715 </assert_contents>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	716 </element>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	717 <element name="edgeR_(2Mut_3WT)-WT" ftype="tabular">
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	718 <assert_contents>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	719 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR"/>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	720 </assert_contents>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	721 </element>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	722 </output_collection>
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	723 </test>
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	724 <!-- Test interaction contrasts with extended dataset (tests make.names fix for interaction terms) -->
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	725 <test expect_num_outputs="2">
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	726 <param name="input\|format" value="matrix"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	727 <param name="input\|counts" value="matrix-extended.txt"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	728 <param name="input\|fact\|ffile" value="yes"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	729 <param name="input\|fact\|finfo" value="factorinfo-extended.txt"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	730 <param name="formula" value="~ 0 + Genotype:Batch"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	731 <param name="contrasts\|contrastOpt" value="manual"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	732 <repeat name="contrasts\|rep_contrast">
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	733 <param name="contrast" value="Mut:b1-WT:b1"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	734 </repeat>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	735 <repeat name="contrasts\|rep_contrast">
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	736 <param name="contrast" value="Mut:b2-Mut:b3"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	737 </repeat>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	738 <param name="adv\|normalisationOption" value="TMM"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	739 <output_collection name="outTables" count="2">
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	740 <element name="edgeR_Mut.b1-WT.b1" ftype="tabular">
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	741 <assert_contents>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	742 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	743 <has_text_matching expression="11304"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	744 </assert_contents>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	745 </element>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	746 <element name="edgeR_Mut.b2-Mut.b3" ftype="tabular">
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	747 <assert_contents>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	748 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	749 <has_text_matching expression="11304"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	750 </assert_contents>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	751 </element>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	752 </output_collection>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	753 <output name="outReport">
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	754 <assert_contents>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	755 <has_text text="edgeR Analysis Output"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	756 <has_text text="quasi-likelihood"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	757 </assert_contents>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	758 </output>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	759 </test>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	760 <!-- Test full factorial interaction model (tests make.names fix with different interaction formula) -->
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	761 <test expect_num_outputs="2">
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	762 <param name="input\|format" value="matrix"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	763 <param name="input\|counts" value="matrix-extended.txt"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	764 <param name="input\|fact\|ffile" value="yes"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	765 <param name="input\|fact\|finfo" value="factorinfo-extended.txt"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	766 <param name="formula" value="~ Genotype * Batch"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	767 <param name="contrasts\|contrastOpt" value="manual"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	768 <repeat name="contrasts\|rep_contrast">
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	769 <param name="contrast" value="WT:b2"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	770 </repeat>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	771 <repeat name="contrasts\|rep_contrast">
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	772 <param name="contrast" value="WT:b3-WT:b2"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	773 </repeat>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	774 <param name="adv\|normalisationOption" value="TMM"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	775 <output_collection name="outTables" count="2">
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	776 <element name="edgeR_WT.b2" ftype="tabular">
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	777 <assert_contents>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	778 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	779 <has_text_matching expression="11304"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	780 </assert_contents>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	781 </element>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	782 <element name="edgeR_WT.b3-WT.b2" ftype="tabular">
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	783 <assert_contents>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	784 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	785 <has_text_matching expression="11304"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	786 </assert_contents>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	787 </element>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	788 </output_collection>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	789 <output name="outReport">
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	790 <assert_contents>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	791 <has_text text="edgeR Analysis Output"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	792 <has_text text="quasi-likelihood"/>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	793 </assert_contents>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	794 </output>
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	795 </test>
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	796 </tests>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	797 <help><![CDATA[
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	798 .. class:: infomark
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	799
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	800 What it does
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	801
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	802 Given a counts matrix, or a set of counts files, for example from featureCounts, and optional information about the genes, this tool
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	803 produces plots and tables useful in the analysis of differential gene expression.
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	804
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	805 This tool uses the `edgeR`_ quasi-likelihood pipeline (edgeR-quasi) for differential expression analysis. This statistical methodology uses negative binomial generalized linear models, but with F-tests instead of likelihood ratio tests. This method provides stricter error rate control than other negative binomial based pipelines, including the traditional edgeR pipelines or DESeq2. While the limma pipelines are recommended for large-scale datasets, because of their speed and flexibility, the edgeR-quasi pipeline gives better performance in low-count situations. For the data analyzed in this `edgeR workflow article`_ ,the edgeR-quasi, limma-voom and limma-trend pipelines are all equally suitable and give similar results.
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	806
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	807 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	808 .. _edgeR workflow article: https://f1000research.com/articles/5-1438
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	809
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	810 -----
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	811
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	812 Inputs
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	813
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	814 Counts Data:
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	815
6 7cf6248bc173 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 21f0bc6c64129122212a6d182fdf3e360617e629 iuc parents: 5 diff changeset	816 The counts data can either be input as separate counts files (one sample per file) or a single count matrix (one sample per column). The rows correspond to genes, and columns correspond to the counts for the samples. Values must be tab separated, with the first row containing the sample/column labels and the first column containing the row/gene labels. The sample labels must start with a letter. Gene identifiers can be of any type but must be unique and not repeated within a counts file.
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	817
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	818 Example - Separate Count Files:
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	819
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	820 ========== =======
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	821 GeneID WT1
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	822 ---------- -------
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	823 11287 1699
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	824 11298 1905
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	825 11302 6
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	826 11303 2099
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	827 11304 356
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	828 11305 2528
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	829 ========== =======
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	830
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	831 Example - Single Count Matrix:
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	832
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	833 ========== ======= ======= ======= ======== ======== ========
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	834 GeneID WT1 WT2 WT3 Mut1 Mut2 Mut3
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	835 ---------- ------- ------- ------- -------- -------- --------
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	836 11287 1699 1528 1601 1463 1441 1495
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	837 11298 1905 1744 1834 1345 1291 1346
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	838 11302 6 8 7 5 6 5
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	839 11303 2099 1974 2100 1574 1519 1654
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	840 11304 356 312 337 361 397 346
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	841 11305 2528 2438 2493 1762 1942 2027
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	842 ========== ======= ======= ======= ======== ======== ========
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	843
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	844
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	845 Gene Annotations:
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	846 Optional input for gene annotations, this can contain more
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	847 information about the genes than just an ID number. The annotations will
3 2aa9dd87aad3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	848 be available in the differential expression results table and the optional normalised counts table. The file must contain a header row and have the gene IDs in the first column. The number of rows should match that of the counts files, add NA for any gene IDs with no annotation. The Galaxy tool annotateMyIDs can be used to obtain annotations for human, mouse, fly and zebrafish.
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	849
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	850 Example:
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	851
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	852 ========== ========== ===================================================
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	853 GeneID Symbol GeneName
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	854 ---------- ---------- ---------------------------------------------------
3 2aa9dd87aad3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	855 11287 Pzp pregnancy zone protein
2aa9dd87aad3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	856 11298 Aanat arylalkylamine N-acetyltransferase
2aa9dd87aad3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	857 11302 Aatk apoptosis-associated tyrosine kinase
2aa9dd87aad3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	858 11303 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1
2aa9dd87aad3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	859 11304 Abca4 ATP-binding cassette, sub-family A (ABC1), member 4
2aa9dd87aad3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	860 11305 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	861 ========== ========== ===================================================
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	862
4 9a62dbdb122b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	863 Factor Information:
9a62dbdb122b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	864 Enter factor names and groups in the tool form, or provide a tab-separated file that has the names of the samples in the first column and one header row. The sample names must be the same as the names in the columns of the count matrix. The second column should contain the primary factor levels (e.g. WT, Mut) with optional additional columns for any secondary factors.
9a62dbdb122b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	865
9a62dbdb122b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	866 Example:
9a62dbdb122b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	867
9a62dbdb122b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	868 ========== ============ =========
9a62dbdb122b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	869 Sample Genotype Batch
9a62dbdb122b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	870 ---------- ------------ ---------
9a62dbdb122b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	871 WT1 WT b1
9a62dbdb122b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	872 WT2 WT b2
9a62dbdb122b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	873 WT3 WT b3
9a62dbdb122b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	874 Mut1 Mut b1
9a62dbdb122b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	875 Mut2 Mut b2
9a62dbdb122b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	876 Mut3 Mut b3
9a62dbdb122b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	877 ========== ============ =========
9a62dbdb122b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	878
6 7cf6248bc173 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 21f0bc6c64129122212a6d182fdf3e360617e629 iuc parents: 5 diff changeset	879 Factor Name: The name of the experimental factor being investigated e.g. Genotype, Treatment. One factor must be entered, the name should start with a letter and spaces must not be used. Optionally, additional factors can be included, these are variables that might influence your experiment e.g. Batch, Gender, Subject. If additional factors are entered, an additive linear model will be used.
4 9a62dbdb122b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	880
6 7cf6248bc173 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 21f0bc6c64129122212a6d182fdf3e360617e629 iuc parents: 5 diff changeset	881 Groups: The names of the groups for the factor. The names should start with a letter, and only contain letters, numbers and underscores, other characters such as spaces and hyphens must not be used. If entered into the tool form above, the order must be the same as the samples (to which the groups correspond) are listed in the columns of the counts matrix, with the values separated by commas.
4 9a62dbdb122b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	882
14 c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	883 Formula:
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	884 By default the tool will construct a formula for modelling counts based on the contents of the factors files or the factors given.
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	885 This can be overriden by directly providing the EdgeR formula in section named Formula.
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	886
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	887 Contrasts of Interest:
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	888 The contrasts you wish to make between levels.
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	889 A common contrast would be a simple difference between two levels: "Mut-WT"
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	890 represents the difference between the mutant and wild type genotypes.
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	891 Multiple contrasts must be entered separately using the Insert Contrast button, spaces must not be used.
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	892
14 c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	893 Alternatively, you can specify a file with contrasts. The file must contain a header (it's value is irrelevant)
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	894 and one contrast per line on the first column (other columns are ignored). If using this option, make sure to
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	895 remove any contrast section from the manual part, or the tool will fail.
c5fa04118f83 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4b17306763bc8eb92c8967c7b4b57abcc514e670 iuc parents: 13 diff changeset	896
15 119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	897 Working with Interactions:
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	898 When you have multiple factors, you may want to test for interaction effects between them.
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	899 For example, with factors Genotype (Mut, WT) and Batch (b1, b2, b3), you might want to test
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	900 whether the effect of genotype differs between batches.
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	901
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	902 Interaction Formula: To include interaction terms, use the Formula field with one of these patterns:
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	903
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	904 - ``~ Genotype * Batch`` - Full factorial model (main effects + interactions)
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	905 - ``~ Genotype + Batch + Genotype:Batch`` - Equivalent to above
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	906 - ``~ 0 + Genotype:Batch`` - Cell-means model (each group combination separately)
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	907
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	908 The cell-means model (``~ 0 + Genotype:Batch``) is often preferred for testing specific
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	909 group comparisons as it creates individual parameters for each combination (e.g., Mut.b1, WT.b1, etc.).
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	910
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	911 Interaction Contrasts: When using interactions, contrast names will contain colons that get
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	912 converted to dots automatically. For example:
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	913
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	914 Cell-means model contrasts (with ``~ 0 + Genotype:Batch``):
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	915 - Input contrast: ``Mut:b1-WT:b1`` (compare Mut vs WT within batch b1)
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	916 - Input contrast: ``Mut:b2-Mut:b3`` (compare batch b2 vs b3 within Mut genotype)
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	917 - Output file names: ``edgeR_Mut.b1-WT.b1.tsv``, ``edgeR_Mut.b2-Mut.b3.tsv``
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	918
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	919 Full factorial model contrasts (with ``~ Genotype * Batch``):
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	920 - Input contrast: ``WT:b2`` (interaction effect: WT×b2 vs baseline)
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	921 - Input contrast: ``WT:b3-WT:b2`` (compare interaction effects: WT×b3 vs WT×b2)
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	922 - Output file names: ``edgeR_WT.b2.tsv``, ``edgeR_WT.b3-WT.b2.tsv``
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	923
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	924 Using Contrasts Files with Interactions: When using a contrasts file instead of manual entry,
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	925 the same interaction contrast syntax applies. Create a tab-separated file with a header and
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	926 one contrast per line:
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	927
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	928 Example contrasts file for cell-means model::
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	929
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	930 Contrast
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	931 Mut:b1-WT:b1
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	932 Mut:b2-Mut:b3
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	933 WT:b1-WT:b2
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	934
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	935 Example contrasts file for full factorial model::
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	936
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	937 Contrast
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	938 WT:b2
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	939 WT:b3-WT:b2
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	940 WT
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	941
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	942 The colons in contrast names will be automatically converted to dots in output file names,
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	943 regardless of whether contrasts are entered manually or via file.
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	944
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	945 Note: Ensure you have sufficient replicates for interaction models. With n factors each having
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	946 k levels, you need more than n×k samples to estimate interactions properly.
119f41ec0ada planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212 iuc parents: 14 diff changeset	947
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	948 Filter Low Counts:
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	949 Genes with very low counts across all libraries provide little evidence for differential expression.
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	950 In the biological point of view, a gene must be expressed at some minimal level before
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	951 it is likely to be translated into a protein or to be biologically important. In addition, the
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	952 pronounced discreteness of these counts interferes with some of the statistical approximations
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	953 that are used later in the pipeline. These genes should be filtered out prior to further
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	954 analysis.
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	955 As a rule of thumb, genes are dropped if they can’t possibly be expressed in all the samples
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	956 for any of the conditions. Users can set their own definition of genes being expressed. Usually
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	957 a gene is required to have a count of 5-10 in a library to be considered expressed in that
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	958 library. Users should also filter with count-per-million (CPM) rather than filtering on the
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	959 counts directly, as the latter does not account for differences in library sizes between samples.
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	960
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	961 Option to ignore the genes that do not show significant levels of
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	962 expression, this filtering is dependent on two criteria: CPM/count and number of samples. You can specify to filter on CPM (Minimum CPM) or count (Minimum Count) values:
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	963
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	964 * Minimum CPM: This is the minimum count per million that a gene must have in at
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	965 least the number of samples specified under Minimum Samples.
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	966
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	967 * Minimum Count: This is the minimum count that a gene must have. It can be combined with either Filter
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	968 on Total Count or Minimum Samples.
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	969
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	970 * Filter on Total Count: This can be used with the Minimum Count filter to keep genes
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	971 with a minimum total read count.
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	972
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	973 * Minimum Samples: This is the number of samples in which the Minimum CPM/Count
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	974 requirement must be met in order for that gene to be kept.
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	975
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	976 If the Minimum Samples filter is applied, only genes that exhibit a CPM/count greater than the required amount in at least the number of samples specified will be used for analysis. Care should be taken to
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	977 ensure that the sample requirement is appropriate. In the case of an experiment
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	978 with two experimental groups each with two members, if there is a change from
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	979 insignificant CPM/count to significant CPM/count but the sample requirement is set to 3,
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	980 then this will cause that gene to fail the criteria. When in doubt simply do not
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	981 filter or consult the `edgeR workflow article`_ for filtering recommendations.
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	982
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	983 Advanced Options:
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	984
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	985 By default error rate for multiple testing is controlled using Benjamini and
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	986 Hochberg's false discovery rate control at a threshold value of 0.05. However
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	987 there are options to change this to custom values.
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	988
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	989 * Minimum log2-fold-change Required:
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	990 In addition to meeting the requirement for the adjusted statistic for
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	991 multiple testing, the observation must have an absolute log2-fold-change
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	992 greater than this threshold to be considered significant, thus highlighted
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	993 in the MD plot.
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	994
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	995 * Adjusted Threshold:
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	996 Set the threshold for the resulting value of the multiple testing control
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	997 method. Only observations whose statistic falls below this value is
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	998 considered significant, thus highlighted in the MD plot.
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	999
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1000 * P-Value Adjustment Method:
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1001 Change the multiple testing control method, the options are BH(1995) and
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1002 BY(2001) which are both false discovery rate controls. There is also
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1003 Holm(1979) which is a method for family-wise error rate control.
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1004
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1005 Normalisation Method:
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1006 The most obvious technical factor that affects the read counts, other than gene expression
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1007 levels, is the sequencing depth of each RNA sample. edgeR adjusts any differential expression
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1008 analysis for varying sequencing depths as represented by differing library sizes. This is
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1009 part of the basic modeling procedure and flows automatically into fold-change or p-value
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1010 calculations. It is always present, and doesn’t require any user intervention.
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1011 The second most important technical influence on differential expression is one that is less
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1012 obvious. RNA-seq provides a measure of the relative abundance of each gene in each RNA
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1013 sample, but does not provide any measure of the total RNA output on a per-cell basis.
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1014 This commonly becomes important when a small number of genes are very highly expressed
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1015 in one sample, but not in another. The highly expressed genes can consume a substantial
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1016 proportion of the total library size, causing the remaining genes to be under-sampled in that
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1017 sample. Unless this RNA composition effect is adjusted for, the remaining genes may falsely
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1018 appear to be down-regulated in that sample . The edgeR `calcNormFactors` function normalizes for RNA composition by finding a set of scaling factors for the library sizes that minimize the log-fold changes between the samples for most genes. The default method for computing these scale factors uses a trimmed mean of M values (TMM) between each pair of samples. We call the product of the original library size and the scaling factor the effective library size. The effective library size replaces the original library size in all downsteam analyses. TMM is the recommended method for most RNA-Seq data where the majority (more than half) of the genes are believed not differentially expressed between any pair of the samples. You can change the normalisation method under Advanced Options above. For more information, see the `calcNormFactors` section in the `edgeR User's Guide`_.
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1019
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1020 Robust Settings
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1021 Option to use robust settings. Using robust settings (robust=TRUE) with the edgeR estimateDisp and glmQLFit functions is usually recommended to protect against outlier genes. This is turned on by default. Note that it is only used with the quasi-likelihood F test method. For more information, see the `edgeR workflow article`_.
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1022
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1023 Test Method
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1024 Option to use the likelihood ratio test instead of the quasi-likelihood F test. For more information, see the `edgeR workflow article`_.
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1025
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1026 .. _edgeR User's Guide: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1027
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1028 -----
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1029
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1030 Outputs
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1031
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1032 This tool outputs
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1033
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1034 * a table of differentially expressed genes for each contrast of interest
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1035 * a HTML report with plots and additional information
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1036
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1037 Optionally, under Output Options you can choose to output
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1038
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1039 * a normalised counts table
2 3de72f1f78aa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	1040 * the R script used by this tool
0 1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1041 * an RData file
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1042
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1043 -----
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1044
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1045 Citations
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1046
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1047 Please try to cite the appropriate articles when you publish results obtained using software, as such citation is the main means by which the authors receive credit for their work. For the edgeR method itself, please cite Robinson et al., 2010, and for this tool (which was developed from the Galaxy limma-voom tool) please cite Liu et al., 2015.
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1048
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1049 ]]></help>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1050 <citations>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1051 <citation type="doi">10.1093/bioinformatics/btp616</citation>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1052 <citation type="doi">10.1093/nar/gkv412</citation>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1053 </citations>
1844cd48af49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	1054 </tool>

Mercurial > repos > iuc > edger

annotate edger.xml @ 16:09965c918573 draft default tip