Mercurial > repos > bzonnedda > conifer2
changeset 16:558f04d13648 draft
Uploaded
author | bzonnedda |
---|---|
date | Thu, 23 Feb 2017 04:25:31 -0500 |
parents | 8354ca911187 |
children | 866f95468b5b |
files | c_rpkm.xml |
diffstat | 1 files changed, 3 insertions(+), 3 deletions(-) [+] |
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line diff
--- a/c_rpkm.xml Tue Feb 21 06:04:21 2017 -0500 +++ b/c_rpkm.xml Thu Feb 23 04:25:31 2017 -0500 @@ -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 \$CONIFER_PATH/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_PATH/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_PATH/conifer.py analyze + python \${CONIFER_PATH}/conifer.py analyze --probes $probesFile --rpkm_dir rpkm_dir --output $outputFile