Mercurial > repos > bzonnedda > conifer2
changeset 22:15d60c7c9a19 draft
Uploaded
author | bzonnedda |
---|---|
date | Wed, 05 Jul 2017 13:02:55 -0400 |
parents | 7f685fe845e1 |
children | 9196f299dc5e |
files | c_rpkm.xml |
diffstat | 1 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/c_rpkm.xml Wed Jul 05 12:56:11 2017 -0400 +++ b/c_rpkm.xml Wed Jul 05 13:02:55 2017 -0400 @@ -6,20 +6,20 @@ #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 '$__tool_directory__/conifer.py rpkm' + python '$__tool_directory__/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} ${input_bam.inputFile.dataset.name}.bam.bai; - python '$__tool_directory__/conifer.py rpkm' + python '$__tool_directory__/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 '$__tool_directory__/conifer.py analyze' + python '$__tool_directory__/conifer.py' analyze --probes $probesFile --rpkm_dir rpkm_dir --output $outputFile