Mercurial > repos > bzonnedda > conifer2
changeset 14:a899c18be1f6 draft
Uploaded
| author | bzonnedda |
|---|---|
| date | Tue, 21 Feb 2017 06:03:42 -0500 |
| parents | 09ef072c4070 |
| children | 8354ca911187 |
| files | c_rpkm.xml |
| diffstat | 1 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/c_rpkm.xml Tue Feb 21 06:03:27 2017 -0500 +++ b/c_rpkm.xml Tue Feb 21 06:03:42 2017 -0500 @@ -1,25 +1,25 @@ <tool id="conifer_rpkm" name="CoNIFER RPKM and Analyze" version="1.0"> <description></description> - <command interpreter="bash"> + <command> mkdir rpkm_dir; #for $input_bam in $inputs: #if str($input_bam.label.value) != "": ln -s ${input_bam.inputFile} ${$input_bam.label.value}.bam; ln -s ${input_bam.inputFile.metadata.bam_index} ${$input_bam.label.value}.bam.bai; - python ./conifer.py rpkm + python \$CONIFER_PATH/conifer.py rpkm --probes $probesFile --input ${$input_bam.label.value}.bam --output rpkm_dir/${$input_bam.label.value}.txt; #else ln -s ${input_bam.inputFile} ${input_bam.inputFile.dataset.name}.bam; ln -s ${input_bam.inputFile.metadata.bam_index} ${input_bam.inputFile.dataset.name}.bam.bai; - python ./conifer.py rpkm + python \$CONIFER_PATH/conifer.py rpkm --probes $probesFile --input ${input_bam.inputFile.dataset.name}.bam --output rpkm_dir/${input_bam.inputFile.dataset.name}.txt; #end if #end for - python ./conifer.py analyze + python \$CONIFER_PATH/conifer.py analyze --probes $probesFile --rpkm_dir rpkm_dir --output $outputFile