Mercurial > repos > engineson > multiqc
changeset 6:66f1187ed363 draft
planemo upload for repository https://github.com/EnginesOn/galaxy_tools/tree/master/tools/multiqc commit 5260237afe6ac9940e1f45e323d77c3a7c38cc40-dirty
| author | engineson |
|---|---|
| date | Tue, 04 Oct 2016 04:02:10 -0400 |
| parents | a9b6ec207609 |
| children | 4612d775965f |
| files | multiqc.xml |
| diffstat | 1 files changed, 6 insertions(+), 6 deletions(-) [+] |
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--- a/multiqc.xml Tue Jun 21 11:16:05 2016 -0400 +++ b/multiqc.xml Tue Oct 04 04:02:10 2016 -0400 @@ -14,7 +14,7 @@ mkdir multiqc_WDir/${repeat.software}_${i}; - #if $repeat.software == "fastqc" + #if str($repeat.software) == "fastqc" #for $k, $file in enumerate ( $repeat.input_file ) ## create a directory for each file because of the unqiue name file parsing @@ -23,7 +23,7 @@ ln -s ${file} multiqc_WDir/${repeat.software}_${i}/file_$k/fastqc_data.txt; #end for - #else if $repeat.software == "tophat" + #else if str($repeat.software) == "tophat" #for $file in $repeat.input_file ## test if input file name contains align_summary @@ -35,7 +35,7 @@ fi; #end for - #else if $repeat.software == "cutadapt" + #else if str($repeat.software) == "cutadapt" #for $file in $repeat.input_file cat ${file} > multiqc_WDir/${repeat.software}_${i}/'${file.display_name}'.txt; @@ -43,7 +43,7 @@ sed -i 's/You are running/This is/' multiqc_WDir/${repeat.software}_${i}/'${file.display_name}'.txt; #end for - #else if $repeat.software == "featurecounts" + #else if str($repeat.software) == "featurecounts" #for $file in $repeat.input_file ## remove spaces and colon to skip multiqc crash @@ -53,7 +53,7 @@ sed -i 's/ /_/g' multiqc_WDir/${repeat.software}_${i}/featurecounts_result.summary; #end for - #else if $repeat.software == "bismark" + #else if str($repeat.software) == "bismark" #for $file in $repeat.input_file ##cat ${file} > multiqc_WDir/${repeat.software}_${i}/'${file.display_name}'_SE_report.txt; @@ -64,7 +64,7 @@ #for $file in $repeat.input_file cat ${file} > multiqc_WDir/${repeat.software}_${i}/'${file.display_name}'; - #if $repeat.software == "picard" + #if str($repeat.software) == "picard" sed -i 's/picard.sam.markduplicates.MarkDuplicates/picard.sam.MarkDuplicates/' multiqc_WDir/${repeat.software}_${i}/'${file.display_name}'; #end if #end for