Mercurial > repos > bzonnedda > conifer2
changeset 27:02091c92f4f1 draft
Uploaded
| author | bzonnedda |
|---|---|
| date | Thu, 06 Jul 2017 06:29:12 -0400 |
| parents | cbe4551cdc27 |
| children | 629681116b5f |
| files | c_rpkm.xml |
| diffstat | 1 files changed, 8 insertions(+), 4 deletions(-) [+] |
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--- a/c_rpkm.xml Thu Jul 06 06:28:47 2017 -0400 +++ b/c_rpkm.xml Thu Jul 06 06:29:12 2017 -0400 @@ -1,25 +1,29 @@ -<tool id="conifer_rpkm" name="CoNIFER RPKM and Analyze" version="1.0"> +<tool id="conifer_rpkm" name="CoNIFER RPKM and Analyze" version="1.7"> <description></description> +<requirements> + <requirement type="package" version="0.10.0">pysam</requirement> + <requirement type="package" version="3.3.0">pytables</requirement> +</requirements> <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 '$__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