edger: edger.xml annotate

annotate edger.xml @ 1:2a16413ec60d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 22882a8eabae0dcc15938423852d1325303b0b78

author	iuc
date	Tue, 30 Jan 2018 04:07:08 -0500
parents	9bdff28ae1b1
children	a1634a9c2ee1

rev	line source
1 2a16413ec60d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 22882a8eabae0dcc15938423852d1325303b0b78 iuc parents: 0 diff changeset	1 <tool id="edger" name="edgeR" version="3.20.7.0">
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>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	5
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	6 <requirements>
1 2a16413ec60d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 22882a8eabae0dcc15938423852d1325303b0b78 iuc parents: 0 diff changeset	7 <requirement type="package" version="3.20.7">bioconductor-edger</requirement>
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	8 <requirement type="package" version="0.2.15">r-rjson</requirement>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	9 <requirement type="package" version="1.20.0">r-getopt</requirement>
1 2a16413ec60d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 22882a8eabae0dcc15938423852d1325303b0b78 iuc parents: 0 diff changeset	10 <requirement type="package" version="1.4.30">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	11 <!-- required for alpha function used with plotMD -->
1 2a16413ec60d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 22882a8eabae0dcc15938423852d1325303b0b78 iuc parents: 0 diff changeset	12 <requirement type="package" version="0.5.0">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	13 </requirements>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	14
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	15 <version_command><![CDATA[
1 2a16413ec60d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 22882a8eabae0dcc15938423852d1325303b0b78 iuc parents: 0 diff changeset	16 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: ")", 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" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null \| grep -v -i "WARNING: ")
0 9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	17 ]]></version_command>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	18
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	19 <command detect_errors="exit_code"><![CDATA[
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	20 #import json
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	21 Rscript '$__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	22
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	23 -R '$outReport'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	24 -o '$outReport.files_path'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	25
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	26 #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	27
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	28 ## 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	29 #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	30 #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	31 #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	32 #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	33 #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	34 #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	35 $count_files.append(str($file))
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	36 #end for
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	37 $temp_factor.append( {str($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	38 #end for
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	39
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	40 $temp_factor.reverse()
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	41 $temp_factor_names.append([str($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	42 #end for
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	43 -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	44
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	45 #elif $input.format=="matrix":
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	46 -m '$input.counts'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	47 #if $input.fact.ffile=='yes':
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	48 -f '$input.fact.finfo'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	49 #else:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	50 -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	51 #end if
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	52 #end if
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	53
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	54 #if $anno.annoOpt=='yes':
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	55 -a '$anno.geneanno'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	56 #end if
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	57
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	58 -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	59
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	60 #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	61 #if $f.filt.cformat.format_select == 'cpm':
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	62 -c '$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	63 -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	64 #elif $f.filt.cformat.format_select == 'counts':
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	65 -z '$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	66 #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	67 -y
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	68 #elif $f.filt.cformat.samples.count_select == 'sample':
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	69 -s '$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	70 #end if
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	71 #end if
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	72 #end if
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	73
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	74 #if $out.normCounts:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	75 -x
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	76 #end if
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	77 #if $out.rdaOption:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	78 -r
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	79 #end if
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	80
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	81 -l '$adv.lfc'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	82 -p '$adv.pVal'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	83 -d '$adv.pAdjust'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	84 -n '$adv.normalisationOption'
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	85 #if $adv.robOption:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	86 -b
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 $adv.lrtOption:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	89 -t
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	90 #end if
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	91
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	92 &&
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	93 mkdir ./output_dir
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	94
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	95 &&
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	96 cp '$outReport.files_path'/*.tsv output_dir/
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	97 ]]></command>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	98
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	99 <inputs>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	100
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	101 <!-- Counts and Factors -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	102 <conditional name="input">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	103 <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	104 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	105 <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	106 <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	107 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	108
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	109 <when value="files">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	110 <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	111 <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.">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	112 <sanitizer>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	113 <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	114 </sanitizer>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	115 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	116 <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	117 <param name="groupName" type="text" label="Name"
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	118 help="Name of group that the counts files(s) belong to (e.g. WT or Mut). NOTE: Please only use letters, numbers or underscores (case sensitive).">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	119 <sanitizer>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	120 <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	121 </sanitizer>
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 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	124 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	125 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	126 </when>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	127
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	128 <when value="matrix">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	129 <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	130
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	131 <conditional name="fact">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	132 <param name="ffile" type="select" label="Input factor information from file?"
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	133 help="You can choose to input the factor and group information for the samples from a file or manually enter below.">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	134 <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	135 <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	136 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	137 <when value="yes">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	138 <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	139 </when>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	140 <when value="no" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	141 <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	142 <param name="factorName" type="text" label="Factor Name"
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	143 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.">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	144 <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	145 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	146 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	147 <param name="groupNames" type="text" label="Groups"
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	148 help="Enter the group names for the samples separated with commas e.g. WT,WT,WT,Mut,Mut,Mut. The order of the names must match the order of the samples in the columns of the count matrix. NOTE: Please only use letters, numbers or underscores (case sensitive).">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	149 <validator type="empty_field" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	150 <validator type="regex" message="Please only use letters, numbers or underscores, and separate levels by commas">^[\w,]+$</validator>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	151 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	152 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	153 </when>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	154 </conditional>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	155 </when>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	156 </conditional>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	157
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	158 <!-- Gene Annotations -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	159 <conditional name="anno">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	160 <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	161 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	162 <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	163 <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	164 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	165 <when value="yes">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	166 <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	167 </when>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	168 <when value="no" />
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
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	171 <!-- Contrasts -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	172 <repeat name="rep_contrast" title="Contrast" min="1" default="1">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	173 <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 more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	174 <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	175 <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	176 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	177 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	178
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	179 <!-- Filter Options -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	180 <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	181 <conditional name="filt">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	182 <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	183 <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	184 <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	185 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	186 <when value="yes">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	187 <conditional name="cformat">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	188 <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	189 <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	190 <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	191 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	192 <when value="cpm">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	193 <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	194 <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	195 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	196 </when>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	197 <when value="counts">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	198 <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	199 <conditional name="samples">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	200 <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	201 <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	202 <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	203 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	204 <when value="total">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	205 <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	206 </when>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	207 <when value="sample">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	208 <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	209 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	210 </when>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	211 </conditional>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	212 </when>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	213 </conditional>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	214 </when>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	215 <when value="no" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	216 </conditional>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	217 </section>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	218
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	219 <!-- Output Options -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	220 <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	221 <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	222 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	223 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	224 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	225 <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	226 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	227 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	228 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	229 </section>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	230
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	231 <!-- Advanced Options -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	232 <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	233 <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	234 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	235 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	236 <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	237 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	238 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	239 <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	240 <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	241 <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	242 <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	243 <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	244 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	245 <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	246 <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	247 <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	248 <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	249 <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	250 </param>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	251 <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	252 <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	253 </section>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	254
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	255 </inputs>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	256
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	257 <outputs>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	258 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	259 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: Tables">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	260 <discover_datasets pattern="(?P<name>.+)\.tsv$" 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	261 </collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	262 </outputs>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	263
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	264 <tests>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	265 <!-- 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	266 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	267 <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	268 <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	269 <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	270 <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	271 <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	272 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	273 <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	274 <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	275 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	276 <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	277 <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	278 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	279 <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	280 <output_collection name="outTables" count="2">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	281 <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT.tsv" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	282 <element name="edgeR_WT-Mut" ftype="tabular" file="edgeR_WT-Mut.tsv" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	283 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	284 <output name="outReport" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	285 <assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	286 <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	287 <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	288 <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	289 <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	290 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	291 </output>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	292 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	293 <!-- 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	294 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	295 <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	296 <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	297 <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	298 <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	299 <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	300 <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	301 <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	302 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	303 <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	304 <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	305 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	306 <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	307 <output_collection name="outTables" count="1">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	308 <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT_anno.tsv" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	309 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	310 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	311 <!-- Ensure RData file can be output -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	312 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	313 <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	314 <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	315 <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	316 <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	317 <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	318 <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	319 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	320 <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	321 <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	322 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	323 <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	324 <output name="outReport" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	325 <assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	326 <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	327 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	328 </output>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	329 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	330 <!-- 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	331 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	332 <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	333 <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	334 <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	335 <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	336 <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	337 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	338 <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	339 <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	340 <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	341 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	342 <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	343 <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	344 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	345 <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	346 <output_collection name="outTables" count="1" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	347 <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT_2fact.tsv" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	348 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	349 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	350 <!-- Ensure factors file input works -->
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	351 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	352 <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	353 <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	354 <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	355 <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	356 <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	357 <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	358 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	359 <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	360 <output_collection name="outTables" count="1">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	361 <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT_2fact.tsv" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	362 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	363 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	364 <!-- 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	365 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	366 <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	367 <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	368 <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	369 <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	370 <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	371 <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	372 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	373 <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	374 <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	375 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	376 <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	377 <output_collection name="outTables" count="2">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	378 <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT.tsv" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	379 <element name="edgeR_normcounts" ftype="tabular" file="edgeR_normcounts.tsv" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	380 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	381 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	382 <!-- 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	383 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	384 <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	385 <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	386 <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	387 <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	388 <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	389 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	390 <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	391 <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	392 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	393 <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	394 <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	395 <output name="outReport" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	396 <assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	397 <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	398 <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	399 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	400 </output>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	401 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	402 <!-- 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	403 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	404 <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	405 <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	406 <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	407 <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	408 <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	409 <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	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_group">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	412 <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	413 <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	414 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	415 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	416 <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	417 <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	418 <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	419 <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	420 <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	421 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	422 <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	423 <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	424 <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	425 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	426 <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	427 <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	428 <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	429 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	430 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	431 <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	432 <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	433 <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	434 <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	435 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	436 <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	437 <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	438 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	439 <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	440 <output_collection name="outTables" count="3">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	441 <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT_2fact_anno.tsv" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	442 <element name="edgeR_WT-Mut" ftype="tabular" file="edgeR_WT-Mut_2fact_anno.tsv" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	443 <element name="edgeR_normcounts" ftype="tabular" file="edgeR_normcounts_anno.tsv" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	444 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	445 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	446 <!-- 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	447 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	448 <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	449 <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	450 <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	451 <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	452 <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	453 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	454 <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	455 <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	456 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	457 <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	458 <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	459 <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	460 <!-- 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	461 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	462 <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	463 <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	464 <output name="outReport" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	465 <assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	466 <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	467 <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	468 <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	469 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	470 </output>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	471 <output_collection name="outTables" count="1" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	472 <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT_filt.tsv" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	473 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	474 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	475 <!-- 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	476 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	477 <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	478 <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	479 <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	480 <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	481 <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	482 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	483 <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	484 <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	485 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	486 <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	487 <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	488 <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	489 <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	490 <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	491 <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	492 <output name="outReport" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	493 <assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	494 <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	495 <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	496 <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	497 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	498 </output>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	499 <output_collection name="outTables" count="1" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	500 <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT_filt.tsv" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	501 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	502 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	503 <!-- 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	504 <test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	505 <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	506 <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	507 <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	508 <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	509 <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	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_contrast">
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	512 <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	513 </repeat>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	514 <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	515 <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	516 <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	517 <!-- 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	518 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	519 <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	520 <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	521 <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	522 <output name="outReport" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	523 <assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	524 <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	525 <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	526 <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	527 </assert_contents>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	528 </output>
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="1" >
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	530 <element name="edgeR_Mut-WT" ftype="tabular" file="edgeR_Mut-WT_filt.tsv" />
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	531 </output_collection>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	532 </test>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	533 </tests>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	534
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	535 <help><![CDATA[
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	536 .. class:: infomark
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	537
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	538 What it does
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	539
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	540 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	541 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	542
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	543 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	544
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	545 .. _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	546 .. _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	547
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	548 -----
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	549
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	550 Inputs
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	551
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	552 Counts Data:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	553
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	554 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. Gene identifiers can be of any type but must be unique and not repeated within a counts file.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	555
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	556 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	557
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	558 ========== =======
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	559 GeneID WT1
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	560 ---------- -------
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	561 11287 1699
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	562 11298 1905
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	563 11302 6
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	564 11303 2099
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	565 11304 356
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	566 11305 2528
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	567 ========== =======
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	568
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	569 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	570
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	571 ========== ======= ======= ======= ======== ======== ========
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	572 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	573 ---------- ------- ------- ------- -------- -------- --------
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	574 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	575 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	576 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	577 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	578 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	579 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	580 ========== ======= ======= ======= ======== ======== ========
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	581
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	582 Factor Information:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	583 Enter factor names and groups in the tool form, or provide a tab-separated file that has the samples in the same order as listed in the columns of the counts matrix. The second column should contain the primary factor levels (e.g. WT, Mut) with optional additional columns for any secondary factors.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	584
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	585 Example:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	586
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	587 ========== ============ =========
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	588 Sample Genotype Batch
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	589 ---------- ------------ ---------
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	590 WT1 WT b1
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	591 WT2 WT b2
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	592 WT3 WT b3
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	593 Mut1 Mut b1
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	594 Mut2 Mut b2
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	595 Mut3 Mut b3
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	596 ========== ============ =========
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	597
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	598 Factor Name: The name of the experimental factor being investigated e.g. Genotype, Treatment. One factor must be entered 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, edgeR will fit an additive linear model.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	599
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	600 Groups: The names of the groups for the factor. These must be entered in the same order as the samples (to which the groups correspond) are listed in the columns of the counts matrix. Spaces must not be used and if entered into the tool form above, the values should be separated by commas.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	601
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	602
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	603 Gene Annotations:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	604 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	605 information about the genes than just an ID number. The annotations will
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	606 be available in the differential expression results table and the optional normalised counts table.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	607
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	608 Example:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	609
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	610 ========== ========== ===================================================
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	611 GeneID Symbol GeneName
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	612 ---------- ---------- ---------------------------------------------------
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	613 1287 Pzp pregnancy zone protein
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	614 1298 Aanat arylalkylamine N-acetyltransferase
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	615 1302 Aatk apoptosis-associated tyrosine kinase
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	616 1303 Abca1 ATP-binding cassette, sub-family A (ABC1), member 1
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	617 1304 Abca4 ATP-binding cassette, sub-family A (ABC1), member 4
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	618 1305 Abca2 ATP-binding cassette, sub-family A (ABC1), member 2
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	619 ========== ========== ===================================================
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	620
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	621 Contrasts of Interest:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	622 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	623 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	624 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	625 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	626
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	627 Filter Low Counts:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	628 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	629 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	630 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	631 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	632 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	633 analysis.
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	634 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	635 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	636 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	637 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	638 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	639
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	640 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	641 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	642
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	643 * 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	644 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	645
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	646 * 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	647 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	648
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	649 * 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	650 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	651
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	652 * 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	653 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	654
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	655 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	656 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	657 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	658 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	659 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	660 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	661
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	662 Advanced Options:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	663
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	664 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	665 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	666 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	667
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	668 * 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	669 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	670 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	671 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	672 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	673
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	674 * Adjusted Threshold:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	675 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	676 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	677 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	678
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	679 * 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	680 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	681 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	682 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	683
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	684 Normalisation Method:
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	685 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	686 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	687 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	688 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	689 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	690 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	691 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	692 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	693 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	694 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	695 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	696 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	697 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	698
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	699 Robust Settings
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	700 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	701
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	702 Test Method
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	703 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	704
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	705 .. _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	706
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	707 -----
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	708
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	709 Outputs
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 This tool outputs
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 * 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	714 * 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	715
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	716 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	717
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	718 * a normalised counts table
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	719 * an RData file
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	720
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	721 -----
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 Citations
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	724
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	725 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	726
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	727 ]]></help>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	728 <citations>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	729 <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	730 <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	731 </citations>
9bdff28ae1b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit eac022c9c6e51e661c1513306b9fefdad673487d iuc parents: diff changeset	732 </tool>

Mercurial > repos > iuc > edger

annotate edger.xml @ 1:2a16413ec60d draft