edger: edger.xml annotate

annotate edger.xml @ 9:6e53e565fc6a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 8c4b8f8711df0a4d6fa98fa8a6f91b977395d62c"

author	iuc
date	Sat, 26 Jun 2021 19:09:53 +0000
parents	3d89af8a44f0
children	df0c8d0a5992

rev	line source
9 6e53e565fc6a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 8c4b8f8711df0a4d6fa98fa8a6f91b977395d62c" iuc parents: 8 diff changeset	1 <tool id="edger" name="edgeR" version="3.34.0+galaxy1">
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	2 <description>
9bdff28ae1b1 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
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	4 </description>
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 7 diff changeset	5 <xrefs>
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 7 diff changeset	6 <xref type="bio.tools">edger</xref>
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 7 diff changeset	7 </xrefs>
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 7 diff changeset	8 <edam_topics>
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 7 diff changeset	9 <edam_topic>topic_3308</edam_topic>
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 7 diff changeset	10 </edam_topics>
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 7 diff changeset	11 <edam_operations>
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 7 diff changeset	12 <edam_operation>operation_3563</edam_operation>
3d89af8a44f0 "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_3223</edam_operation>
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 7 diff changeset	14 </edam_operations>
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	15
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	16 <requirements>
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 7 diff changeset	17 <requirement type="package" version="3.34.0">bioconductor-edger</requirement>
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 7 diff changeset	18 <requirement type="package" version="3.48.0">bioconductor-limma</requirement>
4 4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	19 <requirement type="package" version="0.2.20">r-rjson</requirement>
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 7 diff changeset	20 <requirement type="package" version="1.20.3">r-getopt</requirement>
3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 7 diff changeset	21 <requirement type="package" version="1.4.36">r-statmod</requirement>
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	22 <!-- required for alpha function used with plotMD -->
8 3d89af8a44f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 215a0f27f3de87506895ac655f801c40e8c7edbc" iuc parents: 7 diff changeset	23 <requirement type="package" version="1.1.1">r-scales</requirement>
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	24 </requirements>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	25
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	26 <version_command><![CDATA[
2 a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	27 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" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null \| grep -v -i "WARNING: ")
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	28 ]]></version_command>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	29
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	30 <command detect_errors="exit_code"><![CDATA[
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	31 #import json
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	32 Rscript '$__tool_directory__/edger.R'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	33
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	34 -R '$outReport'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	35 -o '$outReport.files_path'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	36
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	37 #if $input.format=="files":
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	38
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	39 ## Adapted from DESeq2 wrapper
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	40 #set $temp_factor_names = list()
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	41 #for $fact in $input.rep_factor:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	42 #set $temp_factor = list()
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	43 #for $g in $fact.rep_group:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	44 #set $count_files = list()
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	45 #for $file in $g.countsFile:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	46 $count_files.append(str($file))
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	47 #end for
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	48 $temp_factor.append( {str($g.groupName): $count_files} )
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	49 #end for
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	50
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	51 $temp_factor.reverse()
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	52 $temp_factor_names.append([str($fact.factorName), $temp_factor])
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	53 #end for
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	54 -j '#echo json.dumps(temp_factor_names)#'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	55
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	56 #elif $input.format=="matrix":
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	57 -m '$input.counts'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	58 #if $input.fact.ffile=='yes':
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	59 -f '$input.fact.finfo'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	60 #else:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	61 -i '${ '\|'.join( ['%s::%s' % ($x.factorName, $x.groupNames) for x in $input.fact.rep_factor] ) }'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	62 #end if
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	63 #end if
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	64
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	65 #if $anno.annoOpt=='yes':
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	66 -a '$anno.geneanno'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	67 #end if
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	68
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	69 -C '${ ','.join( ['%s' % $x.contrast for x in $rep_contrast] ) }'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	70
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	71 #if $f.filt.filt_select == 'yes':
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	72 #if $f.filt.cformat.format_select == 'cpm':
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	73 -c '$f.filt.cformat.cpmReq'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	74 -s '$f.filt.cformat.cpmSampleReq'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	75 #elif $f.filt.cformat.format_select == 'counts':
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	76 -z '$f.filt.cformat.cntReq'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	77 #if $f.filt.cformat.samples.count_select == 'total':
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	78 -y
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	79 #elif $f.filt.cformat.samples.count_select == 'sample':
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	80 -s '$f.filt.cformat.samples.cntSampleReq'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	81 #end if
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	82 #end if
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	83 #end if
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	84
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	85 #if $out.normCounts:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	86 -x
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	87 #end if
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	88 #if $out.rdaOption:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	89 -r
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	90 #end if
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	91
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	92 -l '$adv.lfc'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	93 -p '$adv.pVal'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	94 -d '$adv.pAdjust'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	95 -n '$adv.normalisationOption'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	96 #if $adv.robOption:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	97 -b
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	98 #end if
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	99 #if $adv.lrtOption:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	100 -t
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	101 #end if
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	102
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	103 &&
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	104 mkdir ./output_dir
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	105
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	106 &&
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	107 cp '$outReport.files_path'/*.tsv output_dir/
2 a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	108
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	109 #if $out.rscript:
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	110 && cp '$__tool_directory__/edger.R' '$rscript'
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	111 #end if
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	112 ]]></command>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	113
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	114 <inputs>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	115
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	116 <!-- Counts and Factors -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	117 <conditional name="input">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	118 <param name="format" type="select" label="Count Files or Matrix?"
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	119 help="You can choose to input either separate count files (one per sample) or a single count matrix">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	120 <option value="files">Separate Count Files</option>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	121 <option value="matrix">Single Count Matrix</option>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	122 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	123
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	124 <when value="files">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	125 <repeat name="rep_factor" title="Factor" min="1">
6 555659de7321 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 21f0bc6c64129122212a6d182fdf3e360617e629 iuc parents: 5 diff changeset	126 <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">
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	127 <sanitizer>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	128 <valid initial="string.letters,string.digits"><add value="_" /></valid>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	129 </sanitizer>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	130 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	131 <repeat name="rep_group" title="Group" min="2" default="2">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	132 <param name="groupName" type="text" label="Name"
6 555659de7321 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 21f0bc6c64129122212a6d182fdf3e360617e629 iuc parents: 5 diff changeset	133 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">
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	134 <sanitizer>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	135 <valid initial="string.letters,string.digits"><add value="_" /></valid>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	136 </sanitizer>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	137 </param>
3 d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	138 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts files"/>
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	139 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	140 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	141 </when>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	142
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	143 <when value="matrix">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	144 <param name="counts" type="data" format="tabular" label="Count Matrix"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	145
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	146 <conditional name="fact">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	147 <param name="ffile" type="select" label="Input factor information from file?"
6 555659de7321 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 21f0bc6c64129122212a6d182fdf3e360617e629 iuc parents: 5 diff changeset	148 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 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	149 <option value="no">No</option>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	150 <option value="yes">Yes</option>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	151 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	152 <when value="yes">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	153 <param name="finfo" type="data" format="tabular" label="Factor File"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	154 </when>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	155 <when value="no" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	156 <repeat name="rep_factor" title="Factor" min="1">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	157 <param name="factorName" type="text" label="Factor Name"
6 555659de7321 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 21f0bc6c64129122212a6d182fdf3e360617e629 iuc parents: 5 diff changeset	158 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">
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	159 <validator type="empty_field" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	160 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	161 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	162 <param name="groupNames" type="text" label="Groups"
6 555659de7321 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 21f0bc6c64129122212a6d182fdf3e360617e629 iuc parents: 5 diff changeset	163 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">
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	164 <validator type="empty_field" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	165 <validator type="regex" message="Please only use letters, numbers or underscores, and separate levels by commas">^[\w,]+$</validator>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	166 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	167 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	168 </when>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	169 </conditional>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	170 </when>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	171 </conditional>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	172
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	173 <!-- Gene Annotations -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	174 <conditional name="anno">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	175 <param name="annoOpt" type="select" label="Use Gene Annotations?"
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	176 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.">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	177 <option value="no">No</option>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	178 <option value="yes">Yes</option>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	179 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	180 <when value="yes">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	181 <param name="geneanno" type="data" format="tabular" label="Gene Annotations"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	182 </when>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	183 <when value="no" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	184 </conditional>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	185
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	186 <!-- Contrasts -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	187 <repeat name="rep_contrast" title="Contrast" min="1" default="1">
7 334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	188 <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.">
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	189 <validator type="empty_field" />
7 334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	190 <validator type="regex" message="Please only use letters, numbers, parentheses or underscores">^[\w\-()]+$</validator>
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	191 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	192 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	193
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	194 <!-- Filter Options -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	195 <section name="f" expanded="false" title="Filter Low Counts">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	196 <conditional name="filt">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	197 <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">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	198 <option value="no" selected="true">No</option>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	199 <option value="yes">Yes</option>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	200 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	201 <when value="yes">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	202 <conditional name="cformat">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	203 <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. ">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	204 <option value="cpm">CPM</option>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	205 <option value="counts">Counts</option>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	206 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	207 <when value="cpm">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	208 <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."/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	209 <param name="cpmSampleReq" type="integer" value="0" min="0" label="Minimum Samples"
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	210 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."/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	211 </when>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	212 <when value="counts">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	213 <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." />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	214 <conditional name="samples">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	215 <param name="count_select" type="select" label="Filter on Total Count or per Sample Count values?" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	216 <option value="total">Total</option>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	217 <option value="sample">Sample</option>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	218 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	219 <when value="total">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	220 <param name="totReq" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Filter on Total Count" help="Apply the Minimum Count filter to genes after summing counts for all samples. See the Filter Low Counts section below for more information." />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	221 </when>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	222 <when value="sample">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	223 <param name="cntSampleReq" type="integer" value="0" min="0" label="Minimum Samples"
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	224 help="Filter out all genes that do not meet the Minimum Count in at least this many samples. See the Filter Low Counts section below for more information."/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	225 </when>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	226 </conditional>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	227 </when>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	228 </conditional>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	229 </when>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	230 <when value="no" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	231 </conditional>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	232 </section>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	233
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	234 <!-- Output Options -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	235 <section name="out" expanded="false" title="Output Options">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	236 <param name="normCounts" type="boolean" truevalue="1" falsevalue="0" checked="false"
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	237 label="Output Normalised Counts Table?"
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	238 help="Output a file containing the normalised counts, these are in log2 counts per million (logCPM). Default: No">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	239 </param>
2 a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	240 <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"/>
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	241 <param name="rdaOption" type="boolean" truevalue="1" falsevalue="0" checked="false"
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	242 label="Output RData file?"
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	243 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">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	244 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	245 </section>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	246
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	247 <!-- Advanced Options -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	248 <section name="adv" expanded="false" title="Advanced Options">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	249 <param name="lfc" type="float" value="0" min="0"
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	250 label="Minimum Log2 Fold Change"
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	251 help="Genes above this threshold and below the p-value threshold are considered significant and highlighted in the MD plot. Default: 0."/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	252 <param name="pVal" type="float" value="0.05" min="0" max="1"
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	253 label="P-Value Adjusted Threshold"
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	254 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."/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	255 <param name="pAdjust" type="select" label="P-Value Adjustment Method" help="Default: BH">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	256 <option value="BH" selected="true">Benjamini and Hochberg (1995)</option>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	257 <option value="BY">Benjamini and Yekutieli (2001)</option>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	258 <option value="holm">Holm (1979)</option>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	259 <option value="none">None</option>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	260 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	261 <param name="normalisationOption" type="select" label="Normalisation Method" help="Default: TMM">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	262 <option value="TMM" selected="true">TMM</option>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	263 <option value="RLE">RLE</option>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	264 <option value="upperquartile">Upperquartile</option>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	265 <option value="none">None (Don't normalise)</option>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	266 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	267 <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" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	268 <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"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	269 </section>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	270
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	271 </inputs>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	272
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	273 <outputs>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	274 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	275 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: Tables">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	276 <discover_datasets pattern="(?P<name>.+)\.tsv$" format="tabular" directory="output_dir" visible="false" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	277 </collection>
2 a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	278 <data name="rscript" format="txt" label="${tool.name} on ${on_string}: Rscript">
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	279 <filter>out['rscript']</filter>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	280 </data>
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	281 </outputs>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	282
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	283 <tests>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	284 <!-- Ensure report is output -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	285 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	286 <param name="format" value="matrix" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	287 <param name="counts" value="matrix.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	288 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	289 <param name="factorName" value="Genotype"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	290 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	291 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	292 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	293 <param name="contrast" value="Mut-WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	294 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	295 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	296 <param name="contrast" value="WT-Mut" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	297 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	298 <param name="normalisationOption" value="TMM" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	299 <output_collection name="outTables" count="2">
2 a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	300 <element name="edgeR_Mut-WT" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	301 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	302 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	303 <has_text_matching expression="11304.*0.4582" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	304 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	305 </element>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	306 <element name="edgeR_WT-Mut" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	307 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	308 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	309 <has_text_matching expression="11304.*-0.4582" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	310 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	311 </element>
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	312 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	313 <output name="outReport" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	314 <assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	315 <has_text text="edgeR Analysis Output" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	316 <has_text text="quasi-likelihood" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	317 <not_has_text text="likelihood ratio" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	318 <not_has_text text="RData" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	319 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	320 </output>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	321 </test>
7 334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	322 <!-- Complex contrasts constructions -->
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	323 <test>
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	324 <param name="format" value="matrix" />
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	325 <param name="counts" value="matrix-complex.txt" />
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	326 <repeat name="rep_factor">
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	327 <param name="factorName" value="Genotype"/>
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	328 <param name="groupNames" value="MutA,MutA,MutA,MutB,MutB,MutB,WTA,WTA,WTA,WTB,WTB,WTB" />
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	329 </repeat>
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	330 <repeat name="rep_contrast">
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	331 <param name="contrast" value="(MutA-MutB)-(WTA-WTB)" />
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	332 </repeat>
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	333 <param name="normalisationOption" value="TMM" />
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	334 <output_collection name="outTables" count="1">
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	335 <element name="edgeR_(MutA-MutB)-(WTA-WTB)" ftype="tabular" >
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	336 <assert_contents>
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	337 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR" />
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	338 <has_text_matching expression="11304.*15.53" />
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	339 </assert_contents>
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	340 </element>
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	341 </output_collection>
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	342 <output name="outReport" >
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	343 <assert_contents>
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	344 <has_text text="edgeR Analysis Output" />
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	345 <has_text text="quasi-likelihood" />
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	346 <not_has_text text="likelihood ratio" />
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	347 <not_has_text text="RData" />
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	348 </assert_contents>
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	349 </output>
334ce9b1bac5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 106b877ec24a2422c0c13e37bf275c7441108b36 iuc parents: 6 diff changeset	350 </test>
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	351 <!-- Ensure annotation file input works -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	352 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	353 <param name="format" value="matrix" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	354 <param name="annoOpt" value="yes" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	355 <param name="geneanno" value="anno.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	356 <param name="counts" value="matrix.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	357 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	358 <param name="factorName" value="Genotype"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	359 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	360 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	361 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	362 <param name="contrast" value="Mut-WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	363 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	364 <param name="normalisationOption" value="TMM" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	365 <output_collection name="outTables" count="1">
2 a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	366 <element name="edgeR_Mut-WT" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	367 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	368 <has_text_matching expression="EntrezID.Symbol.logFC.logCPM.F.PValue.FDR" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	369 <has_text_matching expression="11304.Abca4.0.4582" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	370 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	371 </element>
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	372 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	373 </test>
2 a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	374 <!-- Ensure RScript and RData file can be output -->
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	375 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	376 <param name="format" value="matrix" />
2 a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	377 <param name="rscript" value="True"/>
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	378 <param name="rdaOption" value="true" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	379 <param name="counts" value="matrix.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	380 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	381 <param name="factorName" value="Genotype"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	382 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	383 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	384 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	385 <param name="contrast" value="Mut-WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	386 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	387 <param name="normalisationOption" value="TMM" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	388 <output name="outReport" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	389 <assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	390 <has_text text="RData" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	391 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	392 </output>
4 4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	393 <output name="rscript">
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	394 <assert_contents>
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	395 <has_text_matching expression="Task run time" />
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	396 </assert_contents>
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	397 </output>
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	398 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	399 <!-- Ensure secondary factors work -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	400 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	401 <param name="format" value="matrix" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	402 <param name="counts" value="matrix.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	403 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	404 <param name="factorName" value="Genotype"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	405 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	406 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	407 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	408 <param name="factorName" value="Batch"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	409 <param name="groupNames" value="b1,b2,b3,b1,b2,b3"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	410 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	411 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	412 <param name="contrast" value="Mut-WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	413 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	414 <param name="normalisationOption" value="TMM" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	415 <output_collection name="outTables" count="1" >
2 a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	416 <element name="edgeR_Mut-WT" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	417 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	418 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	419 <has_text_matching expression="11304.*0.4584" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	420 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	421 </element>
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	422 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	423 </test>
4 4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	424 <!-- Ensure factors file with unordered samples works -->
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	425 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	426 <param name="format" value="matrix" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	427 <param name="ffile" value="yes" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	428 <param name="finfo" value="factorinfo.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	429 <param name="counts" value="matrix.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	430 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	431 <param name="contrast" value="Mut-WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	432 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	433 <param name="normalisationOption" value="TMM" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	434 <output_collection name="outTables" count="1">
2 a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	435 <element name="edgeR_Mut-WT" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	436 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	437 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	438 <has_text_matching expression="11304.*0.4584" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	439 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	440 </element>
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	441 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	442 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	443 <!-- Ensure normalised counts file output works-->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	444 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	445 <param name="format" value="matrix" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	446 <param name="normCounts" value="true" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	447 <param name="counts" value="matrix.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	448 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	449 <param name="factorName" value="Genotype"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	450 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	451 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	452 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	453 <param name="contrast" value="Mut-WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	454 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	455 <param name="normalisationOption" value="TMM" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	456 <output_collection name="outTables" count="2">
2 a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	457 <element name="edgeR_Mut-WT" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	458 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	459 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	460 <has_text_matching expression="11304.*0.4582" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	461 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	462 </element>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	463 <element name="edgeR_normcounts" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	464 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	465 <has_text_matching expression="GeneID.Mut1.Mut2.Mut3.WT1.WT2.WT3" />
5 fb9b9f0f2f06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 91bdcc6a5a46173be6546d590cdf3f311c2b1476 iuc parents: 4 diff changeset	466 <has_text_matching expression="11304.*15.75" />
2 a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	467 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	468 </element>
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	469 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	470 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	471 <!-- Ensure likelihood ratio option works -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	472 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	473 <param name="format" value="matrix" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	474 <param name="counts" value="matrix.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	475 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	476 <param name="factorName" value="Genotype"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	477 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	478 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	479 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	480 <param name="contrast" value="Mut-WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	481 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	482 <param name="normalisationOption" value="TMM" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	483 <param name="lrtOption" value="true" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	484 <output name="outReport" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	485 <assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	486 <has_text text="likelihood ratio" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	487 <not_has_text text="quasi-likelihood" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	488 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	489 </output>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	490 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	491 <!-- Ensure multiple counts files input works -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	492 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	493 <param name="format" value="files" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	494 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	495 <param name="factorName" value="Genotype"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	496 <repeat name="rep_group">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	497 <param name="groupName" value="WT"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	498 <param name="countsFile" value="WT1.counts,WT2.counts,WT3.counts"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	499 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	500 <repeat name="rep_group">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	501 <param name="groupName" value="Mut"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	502 <param name="countsFile" value="Mut1.counts,Mut2.counts,Mut3.counts"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	503 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	504 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	505 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	506 <param name="factorName" value="Batch"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	507 <repeat name="rep_group">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	508 <param name="groupName" value="b1"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	509 <param name="countsFile" value="WT1.counts,Mut1.counts"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	510 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	511 <repeat name="rep_group">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	512 <param name="groupName" value="b2"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	513 <param name="countsFile" value="WT2.counts,Mut2.counts"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	514 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	515 <repeat name="rep_group">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	516 <param name="groupName" value="b3"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	517 <param name="countsFile" value="WT3.counts,Mut3.counts"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	518 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	519 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	520 <param name="annoOpt" value="yes" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	521 <param name="geneanno" value="anno.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	522 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	523 <param name="contrast" value="Mut-WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	524 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	525 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	526 <param name="contrast" value="WT-Mut" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	527 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	528 <param name="normCounts" value="true" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	529 <output_collection name="outTables" count="3">
2 a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	530 <element name="edgeR_Mut-WT" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	531 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	532 <has_text_matching expression="EntrezID.Symbol.logFC.logCPM.F.PValue.FDR" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	533 <has_text_matching expression="11304.Abca4.0.4584" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	534 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	535 </element>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	536 <element name="edgeR_WT-Mut" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	537 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	538 <has_text_matching expression="logFC.logCPM.F.PValue.FDR" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	539 <has_text_matching expression="11304.Abca4.-0.4584" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	540 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	541 </element>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	542 <element name="edgeR_normcounts" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	543 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	544 <has_text_matching expression="Mut1.Mut2.Mut3.WT1.WT2.*WT3" />
5 fb9b9f0f2f06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 91bdcc6a5a46173be6546d590cdf3f311c2b1476 iuc parents: 4 diff changeset	545 <has_text_matching expression="11304.Abca4.15.75" />
2 a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	546 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	547 </element>
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	548 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	549 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	550 <!-- Ensure filtering on CPM in Mnimum Samples works -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	551 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	552 <param name="format" value="matrix" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	553 <param name="counts" value="matrix.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	554 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	555 <param name="factorName" value="Genotype"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	556 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	557 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	558 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	559 <param name="contrast" value="Mut-WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	560 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	561 <param name="normalisationOption" value="TMM" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	562 <param name="filt_select" value="yes" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	563 <param name="format_select" value="cpm" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	564 <!-- real cpmReq values would be a lot lower
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	565 this is just for this tiny test dataset -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	566 <param name="cpmReq" value="1000" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	567 <param name="cpmSampleReq" value="3" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	568 <output name="outReport" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	569 <assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	570 <has_text text="CPM in at least" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	571 <not_has_text text="after summing counts for all samples" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	572 <not_has_text text="counts in at least" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	573 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	574 </output>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	575 <output_collection name="outTables" count="1" >
2 a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	576 <element name="edgeR_Mut-WT" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	577 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	578 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	579 <has_text_matching expression="11304.*0.4568" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	580 <not_has_text text="-0.0682" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	581 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	582 </element>
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	583 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	584 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	585 <!-- Ensure filtering on Count in Minmum Samples works -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	586 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	587 <param name="format" value="matrix" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	588 <param name="counts" value="matrix.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	589 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	590 <param name="factorName" value="Genotype"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	591 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	592 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	593 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	594 <param name="contrast" value="Mut-WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	595 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	596 <param name="normalisationOption" value="TMM" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	597 <param name="filt_select" value="yes" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	598 <param name="format_select" value="counts" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	599 <param name="cntReq" value="10" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	600 <param name="count_select" value="sample" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	601 <param name="cntSampleReq" value="3" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	602 <output name="outReport" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	603 <assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	604 <has_text text="counts in at least" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	605 <not_has_text text="after summing counts for all samples" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	606 <not_has_text text="CPM in at least" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	607 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	608 </output>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	609 <output_collection name="outTables" count="1" >
2 a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	610 <element name="edgeR_Mut-WT" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	611 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	612 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	613 <has_text_matching expression="11304.*0.4568" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	614 <not_has_text text="-0.0682" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	615 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	616 </element>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	617
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	618 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	619 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	620 <!-- Ensure filtering on Total Count works -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	621 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	622 <param name="format" value="matrix" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	623 <param name="counts" value="matrix.txt" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	624 <repeat name="rep_factor">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	625 <param name="factorName" value="Genotype"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	626 <param name="groupNames" value="Mut,Mut,Mut,WT,WT,WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	627 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	628 <repeat name="rep_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	629 <param name="contrast" value="Mut-WT" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	630 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	631 <param name="normalisationOption" value="TMM" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	632 <param name="filt_select" value="yes" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	633 <param name="format_select" value="counts" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	634 <!-- real cntReq values would be a lot lower
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	635 this is just for this tiny test dataset -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	636 <param name="cntReq" value="1000" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	637 <param name="count_select" value="total" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	638 <param name="totReq" value="true" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	639 <output name="outReport" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	640 <assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	641 <has_text text="after summing counts for all samples" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	642 <not_has_text text="counts in at least" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	643 <not_has_text text="CPM in at least" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	644 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	645 </output>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	646 <output_collection name="outTables" count="1" >
2 a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	647 <element name="edgeR_Mut-WT" ftype="tabular" >
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	648 <assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	649 <has_text_matching expression="GeneID.logFC.logCPM.F.PValue.*FDR" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	650 <has_text_matching expression="11304.*0.4568" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	651 <not_has_text text="-0.0682" />
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	652 </assert_contents>
a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	653 </element>
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	654 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	655 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	656 </tests>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	657
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	658 <help><![CDATA[
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	659 .. class:: infomark
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	660
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	661 What it does
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	662
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	663 Given a counts matrix, or a set of counts files, for example from featureCounts, and optional information about the genes, this tool
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	664 produces plots and tables useful in the analysis of differential gene expression.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	665
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	666 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.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	667
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	668 .. _edgeR: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	669 .. _edgeR workflow article: https://f1000research.com/articles/5-1438
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	670
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	671 -----
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	672
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	673 Inputs
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	674
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	675 Counts Data:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	676
6 555659de7321 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 21f0bc6c64129122212a6d182fdf3e360617e629 iuc parents: 5 diff changeset	677 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 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	678
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	679 Example - Separate Count Files:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	680
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	681 ========== =======
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	682 GeneID WT1
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	683 ---------- -------
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	684 11287 1699
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	685 11298 1905
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	686 11302 6
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	687 11303 2099
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	688 11304 356
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	689 11305 2528
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	690 ========== =======
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	691
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	692 Example - Single Count Matrix:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	693
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	694 ========== ======= ======= ======= ======== ======== ========
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	695 GeneID WT1 WT2 WT3 Mut1 Mut2 Mut3
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	696 ---------- ------- ------- ------- -------- -------- --------
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	697 11287 1699 1528 1601 1463 1441 1495
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	698 11298 1905 1744 1834 1345 1291 1346
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	699 11302 6 8 7 5 6 5
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	700 11303 2099 1974 2100 1574 1519 1654
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	701 11304 356 312 337 361 397 346
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	702 11305 2528 2438 2493 1762 1942 2027
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	703 ========== ======= ======= ======= ======== ======== ========
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	704
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	705
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	706 Gene Annotations:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	707 Optional input for gene annotations, this can contain more
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	708 information about the genes than just an ID number. The annotations will
3 d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	709 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 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	710
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	711 Example:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	712
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	713 ========== ========== ===================================================
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	714 GeneID Symbol GeneName
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	715 ---------- ---------- ---------------------------------------------------
3 d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	716 11287 Pzp pregnancy zone protein
d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	717 11298 Aanat arylalkylamine N-acetyltransferase
d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	718 11302 Aatk apoptosis-associated tyrosine kinase
d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	719 11303 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1
d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	720 11304 Abca4 ATP-binding cassette, sub-family A (ABC1), member 4
d79ed3ec25fe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit e646be741e315df9332b5206cec1e47c11370ff1 iuc parents: 2 diff changeset	721 11305 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	722 ========== ========== ===================================================
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	723
4 4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	724 Factor Information:
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	725 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.
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	726
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	727 Example:
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	728
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	729 ========== ============ =========
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	730 Sample Genotype Batch
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	731 ---------- ------------ ---------
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	732 WT1 WT b1
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	733 WT2 WT b2
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	734 WT3 WT b3
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	735 Mut1 Mut b1
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	736 Mut2 Mut b2
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	737 Mut3 Mut b3
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	738 ========== ============ =========
4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	739
6 555659de7321 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 21f0bc6c64129122212a6d182fdf3e360617e629 iuc parents: 5 diff changeset	740 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 4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	741
6 555659de7321 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 21f0bc6c64129122212a6d182fdf3e360617e629 iuc parents: 5 diff changeset	742 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 4730985c816f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 230fc767e2e402ee460440afab0e348f2ccab179 iuc parents: 3 diff changeset	743
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	744 Contrasts of Interest:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	745 The contrasts you wish to make between levels.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	746 A common contrast would be a simple difference between two levels: "Mut-WT"
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	747 represents the difference between the mutant and wild type genotypes.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	748 Multiple contrasts must be entered separately using the Insert Contrast button, spaces must not be used.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	749
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	750 Filter Low Counts:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	751 Genes with very low counts across all libraries provide little evidence for differential expression.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	752 In the biological point of view, a gene must be expressed at some minimal level before
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	753 it is likely to be translated into a protein or to be biologically important. In addition, the
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	754 pronounced discreteness of these counts interferes with some of the statistical approximations
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	755 that are used later in the pipeline. These genes should be filtered out prior to further
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	756 analysis.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	757 As a rule of thumb, genes are dropped if they can’t possibly be expressed in all the samples
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	758 for any of the conditions. Users can set their own definition of genes being expressed. Usually
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	759 a gene is required to have a count of 5-10 in a library to be considered expressed in that
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	760 library. Users should also filter with count-per-million (CPM) rather than filtering on the
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	761 counts directly, as the latter does not account for differences in library sizes between samples.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	762
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	763 Option to ignore the genes that do not show significant levels of
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	764 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:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	765
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	766 * Minimum CPM: This is the minimum count per million that a gene must have in at
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	767 least the number of samples specified under Minimum Samples.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	768
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	769 * Minimum Count: This is the minimum count that a gene must have. It can be combined with either Filter
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	770 on Total Count or Minimum Samples.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	771
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	772 * Filter on Total Count: This can be used with the Minimum Count filter to keep genes
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	773 with a minimum total read count.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	774
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	775 * Minimum Samples: This is the number of samples in which the Minimum CPM/Count
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	776 requirement must be met in order for that gene to be kept.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	777
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	778 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
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	779 ensure that the sample requirement is appropriate. In the case of an experiment
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	780 with two experimental groups each with two members, if there is a change from
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	781 insignificant CPM/count to significant CPM/count but the sample requirement is set to 3,
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	782 then this will cause that gene to fail the criteria. When in doubt simply do not
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	783 filter or consult the `edgeR workflow article`_ for filtering recommendations.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	784
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	785 Advanced Options:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	786
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	787 By default error rate for multiple testing is controlled using Benjamini and
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	788 Hochberg's false discovery rate control at a threshold value of 0.05. However
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	789 there are options to change this to custom values.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	790
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	791 * Minimum log2-fold-change Required:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	792 In addition to meeting the requirement for the adjusted statistic for
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	793 multiple testing, the observation must have an absolute log2-fold-change
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	794 greater than this threshold to be considered significant, thus highlighted
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	795 in the MD plot.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	796
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	797 * Adjusted Threshold:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	798 Set the threshold for the resulting value of the multiple testing control
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	799 method. Only observations whose statistic falls below this value is
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	800 considered significant, thus highlighted in the MD plot.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	801
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	802 * P-Value Adjustment Method:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	803 Change the multiple testing control method, the options are BH(1995) and
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	804 BY(2001) which are both false discovery rate controls. There is also
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	805 Holm(1979) which is a method for family-wise error rate control.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	806
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	807 Normalisation Method:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	808 The most obvious technical factor that affects the read counts, other than gene expression
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	809 levels, is the sequencing depth of each RNA sample. edgeR adjusts any differential expression
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	810 analysis for varying sequencing depths as represented by differing library sizes. This is
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	811 part of the basic modeling procedure and flows automatically into fold-change or p-value
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	812 calculations. It is always present, and doesn’t require any user intervention.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	813 The second most important technical influence on differential expression is one that is less
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	814 obvious. RNA-seq provides a measure of the relative abundance of each gene in each RNA
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	815 sample, but does not provide any measure of the total RNA output on a per-cell basis.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	816 This commonly becomes important when a small number of genes are very highly expressed
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	817 in one sample, but not in another. The highly expressed genes can consume a substantial
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	818 proportion of the total library size, causing the remaining genes to be under-sampled in that
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	819 sample. Unless this RNA composition effect is adjusted for, the remaining genes may falsely
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	820 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`_.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	821
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	822 Robust Settings
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	823 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`_.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	824
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	825 Test Method
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	826 Option to use the likelihood ratio test instead of the quasi-likelihood F test. For more information, see the `edgeR workflow article`_.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	827
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	828 .. _edgeR User's Guide: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	829
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	830 -----
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	831
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	832 Outputs
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	833
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	834 This tool outputs
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	835
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	836 * a table of differentially expressed genes for each contrast of interest
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	837 * a HTML report with plots and additional information
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	838
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	839 Optionally, under Output Options you can choose to output
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	840
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	841 * a normalised counts table
2 a1634a9c2ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 910ffba48cb5f981aad1e00b77056bbbec7f9617 iuc parents: 1 diff changeset	842 * the R script used by this tool
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	843 * an RData file
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	844
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	845 -----
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	846
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	847 Citations
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	848
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	849 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.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	850
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	851 ]]></help>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	852 <citations>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	853 <citation type="doi">10.1093/bioinformatics/btp616</citation>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	854 <citation type="doi">10.1093/nar/gkv412</citation>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	855 </citations>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	856 </tool>

Mercurial > repos > iuc > edger

annotate edger.xml @ 9:6e53e565fc6a draft