Repository revision
15:5bf899c13979

Repository 'edger'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/edger

edgeR tool metadata
Miscellaneous
edgeR
Perform differential expression of count data
edger
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy4
3.36.0+galaxy4
echo $(R --version | grep version | grep -v GNU)", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy4 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy3
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.34.0+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.34.0+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.34.0
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.22.5
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.20.7.2
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.20.7.1
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.20.7.0
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.16.5
edger
Requirements (dependencies defined in the <requirements> tag set)
name version type
bioconductor-edger 3.36.0 package
bioconductor-limma 3.50.0 package
r-rjson 0.2.20 package
r-getopt 1.20.3 package
r-statmod 1.4.36 package
r-scales 1.1.1 package
Additional information about this tool
#import json
Rscript '$__tool_directory__/edger.R'

-R '$outReport'
-o '$outReport.files_path'

#if $input.format=="files":

    ## Adapted from DESeq2 wrapper
    #set $temp_factor_names = list()
    #for $fact in $input.rep_factor:
        #set $temp_factor = list()
        #for $g in $fact.rep_group:
            #set $count_files = list()
            #for $file in $g.countsFile:
                $count_files.append(str($file))
            #end for
            $temp_factor.append( {str($g.groupName): $count_files} )
        #end for

        $temp_factor.reverse()
        $temp_factor_names.append([str($fact.factorName), $temp_factor])
    #end for
    -j '#echo json.dumps(temp_factor_names)#'

#elif $input.format=="matrix":
    -m '$input.counts'
    #if $input.fact.ffile=='yes':
        -f '$input.fact.finfo'
    #else:
        -i '${ '|'.join( ['%s::%s' % ($x.factorName, $x.groupNames) for x in $input.fact.rep_factor] ) }'
    #end if
#end if

#if $anno.annoOpt=='yes':
    -a '$anno.geneanno'
#end if

#if $formula:
    -F '$formula'
#end if

#if $contrasts.contrastOpt == 'file':
    -C '$contrasts.cinfo'
#else: 
    -C '${ ','.join( ['%s' % $x.contrast for x in $contrasts.rep_contrast] ) }'
#end if

#if $f.filt.filt_select == 'yes':
    #if $f.filt.cformat.format_select == 'cpm':
        -c '$f.filt.cformat.cpmReq'
        -s '$f.filt.cformat.cpmSampleReq'
    #elif $f.filt.cformat.format_select == 'counts':
            -z '$f.filt.cformat.cntReq'
        #if $f.filt.cformat.samples.count_select == 'total':
            -y
        #elif $f.filt.cformat.samples.count_select == 'sample':
            -s '$f.filt.cformat.samples.cntSampleReq'
        #end if
    #end if
#end if

#if $out.normCounts:
    -x
#end if
#if $out.rdaOption:
    -r
#end if

-l '$adv.lfc'
-p '$adv.pVal'
-d '$adv.pAdjust'
-n '$adv.normalisationOption'
#if $adv.robOption:
    -b
#end if
#if $adv.lrtOption:
    -t
#end if

&&
mkdir ./output_dir

&&
cp '$outReport.files_path'/*.tsv output_dir/

#if $out.rscript:
    && cp '$__tool_directory__/edger.R' '$rscript'
#end if
    
None
False
Functional tests
name inputs outputs required files
Test-1 input|counts: matrix.txt
input|fact|rep_factor_0|factorName: Genotype
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|format: matrix
contrasts|rep_contrast_0|contrast: Mut-WT
contrasts|rep_contrast_1|contrast: WT-Mut
contrasts|contrastOpt: manual
adv|normalisationOption: TMM
name: value
matrix.txt
value
Test-2 input|counts: matrix-complex.txt
input|fact|rep_factor_0|factorName: Genotype
input|fact|rep_factor_0|groupNames: MutA,MutA,MutA,MutB,MutB,MutB,WTA,WTA,WTA,WTB,WTB,WTB
input|format: matrix
contrasts|rep_contrast_0|contrast: (MutA-MutB)-(WTA-WTB)
contrasts|contrastOpt: manual
adv|normalisationOption: TMM
name: value
matrix-complex.txt
value
Test-3 input|counts: matrix.txt
input|fact|rep_factor_0|factorName: Genotype
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|format: matrix
anno|geneanno: anno.txt
anno|annoOpt: yes
contrasts|rep_contrast_0|contrast: Mut-WT
contrasts|contrastOpt: manual
adv|normalisationOption: TMM
matrix.txt
anno.txt
Test-4 input|counts: matrix.txt
input|fact|rep_factor_0|factorName: Genotype
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|format: matrix
contrasts|rep_contrast_0|contrast: Mut-WT
contrasts|contrastOpt: manual
out|rscript: True
out|rdaOption: True
adv|normalisationOption: TMM
name: value
name: value
matrix.txt
value
Test-5 input|counts: matrix.txt
input|fact|rep_factor_0|factorName: Genotype
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|fact|rep_factor_1|factorName: Batch
input|fact|rep_factor_1|groupNames: b1,b2,b3,b1,b2,b3
input|format: matrix
contrasts|rep_contrast_0|contrast: Mut-WT
contrasts|contrastOpt: manual
adv|normalisationOption: TMM
matrix.txt
Test-6 input|counts: matrix.txt
input|fact|finfo: factorinfo.txt
input|fact|ffile: yes
input|format: matrix
contrasts|rep_contrast_0|contrast: Mut-WT
contrasts|contrastOpt: manual
adv|normalisationOption: TMM
matrix.txt
factorinfo.txt
Test-7 input|counts: matrix.txt
input|fact|rep_factor_0|factorName: Genotype
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|format: matrix
contrasts|rep_contrast_0|contrast: Mut-WT
contrasts|contrastOpt: manual
out|normCounts: True
adv|normalisationOption: TMM
matrix.txt
Test-8 input|counts: matrix.txt
input|fact|rep_factor_0|factorName: Genotype
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|format: matrix
contrasts|rep_contrast_0|contrast: Mut-WT
contrasts|contrastOpt: manual
adv|normalisationOption: TMM
adv|lrtOption: True
name: value
matrix.txt
value
Test-9 input|rep_factor_0|factorName: Genotype
input|rep_factor_0|rep_group_0|groupName: WT
input|rep_factor_0|rep_group_0|countsFile: ['WT1.counts', 'WT2.counts', 'WT3.counts']
input|rep_factor_0|rep_group_1|groupName: Mut
input|rep_factor_0|rep_group_1|countsFile: ['Mut1.counts', 'Mut2.counts', 'Mut3.counts']
input|rep_factor_1|factorName: Batch
input|rep_factor_1|rep_group_0|groupName: b1
input|rep_factor_1|rep_group_0|countsFile: ['WT1.counts', 'Mut1.counts']
input|rep_factor_1|rep_group_1|groupName: b2
input|rep_factor_1|rep_group_1|countsFile: ['WT2.counts', 'Mut2.counts']
input|rep_factor_1|rep_group_2|groupName: b3
input|rep_factor_1|rep_group_2|countsFile: ['WT3.counts', 'Mut3.counts']
input|format: files
anno|geneanno: anno.txt
anno|annoOpt: yes
contrasts|rep_contrast_0|contrast: Mut-WT
contrasts|rep_contrast_1|contrast: WT-Mut
contrasts|contrastOpt: manual
out|normCounts: True
WT1.counts
WT2.counts
WT3.counts
Mut1.counts
Mut2.counts
Mut3.counts
WT1.counts
Mut1.counts
WT2.counts
Mut2.counts
WT3.counts
Mut3.counts
anno.txt
Test-10 input|counts: matrix.txt
input|fact|rep_factor_0|factorName: Genotype
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|format: matrix
contrasts|rep_contrast_0|contrast: Mut-WT
contrasts|contrastOpt: manual
f|filt|cformat|cpmReq: 1000
f|filt|cformat|cpmSampleReq: 3
f|filt|cformat|format_select: cpm
f|filt|filt_select: yes
adv|normalisationOption: TMM
name: value
matrix.txt
value
Test-11 input|counts: matrix.txt
input|fact|rep_factor_0|factorName: Genotype
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|format: matrix
contrasts|rep_contrast_0|contrast: Mut-WT
contrasts|contrastOpt: manual
f|filt|cformat|cntReq: 10
f|filt|cformat|samples|cntSampleReq: 3
f|filt|cformat|samples|count_select: sample
f|filt|cformat|format_select: counts
f|filt|filt_select: yes
adv|normalisationOption: TMM
name: value
matrix.txt
value
Test-12 input|counts: matrix.txt
input|fact|rep_factor_0|factorName: Genotype
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|format: matrix
contrasts|rep_contrast_0|contrast: Mut-WT
contrasts|contrastOpt: manual
f|filt|cformat|cntReq: 1000
f|filt|cformat|samples|count_select: total
f|filt|cformat|format_select: counts
f|filt|filt_select: yes
adv|normalisationOption: TMM
name: value
matrix.txt
value
Test-13 input|counts: matrix.txt
input|fact|rep_factor_0|factorName: Genotype
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|fact|rep_factor_1|factorName: Batch
input|fact|rep_factor_1|groupNames: b1,b2,b3,b1,b2,b3
input|format: matrix
formula: ~ 0 + Genotype + Batch
contrasts|cinfo: contrasts_file.txt
contrasts|contrastOpt: file
adv|normalisationOption: TMM
matrix.txt
contrasts_file.txt