| Previous changeset 33:073c77ce5e94 (2013-10-15) Next changeset 35:ff21a055413b (2014-07-22) |
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Commit message:
Patch from Bjorn Gruning |
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modified:
bam2wig.xml |
| b |
| diff -r 073c77ce5e94 -r 8fbd165f8835 bam2wig.xml --- a/bam2wig.xml Tue Oct 15 12:58:55 2013 -0400 +++ b/bam2wig.xml Mon Nov 04 16:19:36 2013 -0500 |
| b |
| @@ -8,15 +8,12 @@ <requirement type="package" version="2.3.7">rseqc</requirement> </requirements> <command> + tmp_input_name=\$(mktemp -u); + bai='.bai'; - #import tempfile, os - #set $tmp_input = tempfile.NamedTemporaryFile() - #set $tmp_input_name = $input_singles_tmp_handle.name - #silent $tmp_input.close() - - ln -s "${input}" $tmp_input_name && - ln -s "${input.metadata.bam_index}" $tmp_input_name + ".bai" && - bam2wig.py -i "local_input.bam" -s $chromsize -o outfile + ln -s "${input}" \$tmp_input_name && + ln -s "${input.metadata.bam_index}" \$tmp_input_name\$bai && + bam2wig.py -i \$tmp_input_name -s $chromsize -o outfile #if str($strand_type.strand_specific) == "pair" -d @@ -44,8 +41,8 @@ -u #end if ; - rm $tmp_input_name + ".bai" ; - rm $tmp_input_name + rm "\$tmp_input_name\$bai"; + rm \$tmp_input_name </command> <inputs> <param name="input" type="data" label="Input .bam File" format="bam" /> |