| Previous changeset 0:9bdff28ae1b1 (2017-11-07) Next changeset 2:a1634a9c2ee1 (2018-04-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 22882a8eabae0dcc15938423852d1325303b0b78 |
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modified:
edger.R edger.xml test-data/edgeR_Mut-WT_2fact.tsv test-data/edgeR_Mut-WT_2fact_anno.tsv test-data/edgeR_WT-Mut_2fact_anno.tsv |
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| diff -r 9bdff28ae1b1 -r 2a16413ec60d edger.R --- a/edger.R Tue Nov 07 08:18:14 2017 -0500 +++ b/edger.R Tue Jan 30 04:07:08 2018 -0500 |
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| @@ -486,9 +486,9 @@ sumStatus <- summary(status) # Collect counts for differential expression - upCount[i] <- sumStatus["1", ] - downCount[i] <- sumStatus["-1", ] - flatCount[i] <- sumStatus["0", ] + upCount[i] <- sumStatus["Up"] + downCount[i] <- sumStatus["Down"] + flatCount[i] <- sumStatus["NotSig"] # Write top expressions table top <- topTags(res, n=Inf, sort.by="PValue") |
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| diff -r 9bdff28ae1b1 -r 2a16413ec60d edger.xml --- a/edger.xml Tue Nov 07 08:18:14 2017 -0500 +++ b/edger.xml Tue Jan 30 04:07:08 2018 -0500 |
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| @@ -1,20 +1,19 @@ -<tool id="edger" name="edgeR" version="3.16.5"> +<tool id="edger" name="edgeR" version="3.20.7.0"> <description> Perform differential expression of count data </description> <requirements> - <requirement type="package" version="3.16.5">bioconductor-edger</requirement> + <requirement type="package" version="3.20.7">bioconductor-edger</requirement> <requirement type="package" version="0.2.15">r-rjson</requirement> <requirement type="package" version="1.20.0">r-getopt</requirement> + <requirement type="package" version="1.4.30">r-statmod</requirement> <!-- required for alpha function used with plotMD --> - <requirement type="package" version="0.4.1">r-scales</requirement> - <!-- This should be in limma conda now - check why still needed? --> - <requirement type="package" version="1.4.30">r-statmod</requirement> + <requirement type="package" version="0.5.0">r-scales</requirement> </requirements> <version_command><![CDATA[ - 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: ") +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: ") ]]></version_command> <command detect_errors="exit_code"><![CDATA[ |
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| diff -r 9bdff28ae1b1 -r 2a16413ec60d test-data/edgeR_Mut-WT_2fact.tsv --- a/test-data/edgeR_Mut-WT_2fact.tsv Tue Nov 07 08:18:14 2017 -0500 +++ b/test-data/edgeR_Mut-WT_2fact.tsv Tue Jan 30 04:07:08 2018 -0500 |
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| @@ -1,7 +1,7 @@ "GeneID" "logFC" "logCPM" "F" "PValue" "FDR" -"11287" 0.189281291475186 17.6499778192954 198.646314971919 7.90598427634257e-09 4.74359056580554e-08 +"11287" 0.189281291475186 17.6499778192954 198.646314971919 7.90598427634242e-09 4.74359056580545e-08 "11298" -0.13798041694802 17.6843133699537 96.2224552671758 4.15830411749776e-06 1.24749123524933e-05 "11304" 0.458490715244216 15.526484673111 14.5864146735617 0.00244295799161999 0.00488591598323999 -"11303" -0.0560600217169691 17.8909334307093 6.5300693781724 0.0442859767053646 0.0664289650580469 -"11305" -0.0585095825423414 18.1629882429457 1.07140336604322 0.32103822810743 0.385245873728916 -"11302" -0.0716631320244627 10.0898336653124 0.376796260571098 0.878304702615846 0.878304702615846 +"11303" -0.0560600217169691 17.8909334307093 6.53006937817236 0.0442859767053646 0.0664289650580469 +"11305" -0.0585095825423414 18.1629882429457 1.07140336604322 0.32103822810743 0.385245873728915 +"11302" -0.0716631320244627 10.0898336653124 0.376796260569999 0.878304702615846 0.878304702615846 |
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| diff -r 9bdff28ae1b1 -r 2a16413ec60d test-data/edgeR_Mut-WT_2fact_anno.tsv --- a/test-data/edgeR_Mut-WT_2fact_anno.tsv Tue Nov 07 08:18:14 2017 -0500 +++ b/test-data/edgeR_Mut-WT_2fact_anno.tsv Tue Jan 30 04:07:08 2018 -0500 |
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| @@ -1,7 +1,7 @@ "EntrezID" "Symbol" "GeneName" "Chr" "Length" "logFC" "logCPM" "F" "PValue" "FDR" -11287 "Pzp" "pregnancy zone protein" 6 4681 0.189281947498313 17.6499778192954 198.646315096405 7.90598424818912e-09 4.74359054891347e-08 +11287 "Pzp" "pregnancy zone protein" 6 4681 0.189281947498313 17.6499778192954 198.646315096405 7.90598424818915e-09 4.74359054891349e-08 11298 "Aanat" "arylalkylamine N-acetyltransferase" 11 1455 -0.137980416947824 17.6843133699537 96.2224553233548 4.15830411749738e-06 1.24749123524921e-05 11304 "Abca4" "ATP-binding cassette, sub-family A (ABC1), member 4" 3 7248 0.45849071524422 15.526484673111 14.5864146737822 0.00244295799149183 0.00488591598298366 11303 "Abca1" "ATP-binding cassette, sub-family A (ABC1), member 1" 4 10260 -0.0560600215744048 17.8909334307093 6.53006938009001 0.0442859767053567 0.066428965058035 11305 "Abca2" "ATP-binding cassette, sub-family A (ABC1), member 2" 2 8061 -0.0585095828508861 18.1629882429457 1.07140336564628 0.321038228193371 0.385245873832045 -11302 "Aatk" "apoptosis-associated tyrosine kinase" 11 5743 -0.0716631320197652 10.0898336653124 0.376796260576848 0.878304702615841 0.878304702615841 +11302 "Aatk" "apoptosis-associated tyrosine kinase" 11 5743 -0.0716631320197652 10.0898336653124 0.376796260576849 0.878304702615839 0.878304702615839 |
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| diff -r 9bdff28ae1b1 -r 2a16413ec60d test-data/edgeR_WT-Mut_2fact_anno.tsv --- a/test-data/edgeR_WT-Mut_2fact_anno.tsv Tue Nov 07 08:18:14 2017 -0500 +++ b/test-data/edgeR_WT-Mut_2fact_anno.tsv Tue Jan 30 04:07:08 2018 -0500 |
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| @@ -1,7 +1,7 @@ "EntrezID" "Symbol" "GeneName" "Chr" "Length" "logFC" "logCPM" "F" "PValue" "FDR" -11287 "Pzp" "pregnancy zone protein" 6 4681 -0.189281947498313 17.6499778192954 198.646315096405 7.90598424818912e-09 4.74359054891347e-08 +11287 "Pzp" "pregnancy zone protein" 6 4681 -0.189281947498313 17.6499778192954 198.646315096405 7.90598424818915e-09 4.74359054891349e-08 11298 "Aanat" "arylalkylamine N-acetyltransferase" 11 1455 0.137980416947824 17.6843133699537 96.2224553233548 4.15830411749738e-06 1.24749123524921e-05 11304 "Abca4" "ATP-binding cassette, sub-family A (ABC1), member 4" 3 7248 -0.45849071524422 15.526484673111 14.5864146737822 0.00244295799149183 0.00488591598298366 11303 "Abca1" "ATP-binding cassette, sub-family A (ABC1), member 1" 4 10260 0.0560600215744048 17.8909334307093 6.53006938009001 0.0442859767053567 0.066428965058035 11305 "Abca2" "ATP-binding cassette, sub-family A (ABC1), member 2" 2 8061 0.0585095828508861 18.1629882429457 1.07140336564628 0.321038228193371 0.385245873832045 -11302 "Aatk" "apoptosis-associated tyrosine kinase" 11 5743 0.0716631320197652 10.0898336653124 0.376796260576848 0.878304702615841 0.878304702615841 +11302 "Aatk" "apoptosis-associated tyrosine kinase" 11 5743 0.0716631320197652 10.0898336653124 0.376796260576849 0.878304702615839 0.878304702615839 |