Mercurial > repos > bgruening > deeptools_compute_matrix
diff computeMatrix.xml @ 12:babca70c3586 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
author | bgruening |
---|---|
date | Fri, 31 Mar 2017 09:28:45 -0400 |
parents | 6f334c8bd52f |
children | 5335711251f6 |
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--- a/computeMatrix.xml Tue Jan 24 04:59:41 2017 -0500 +++ b/computeMatrix.xml Fri Mar 31 09:28:45 2017 -0400 @@ -7,17 +7,20 @@ <expand macro="requirements" /> <command> <![CDATA[ + #import re #import tempfile #set bw_files=[] - #for $counter, $bigwig in enumerate($scoreFileName): - ln -s "${bigwig}" "file_${counter}.bw" && - #silent $bw_files.append('file_%s.bw' % $counter) + #for $counter, $bigwig, in enumerate($scoreFileName): + #set identifier = re.sub('[^\s\w\-]', '_', str($bigwig.element_identifier)) + ln -f -s "${bigwig}" "${identifier}_${counter}.bw" && + #silent $bw_files.append('%s_%s.bw' % ($identifier, $counter)) #end for #set bed_files=[] - #for $counter, $rf in enumerate($regionsFiles): - ln -s "${rf.regionsFile}" "group_${counter}.bed" && - #silent $bed_files.append('group_%s.bed' % $counter) + #for $counter, $rf, in enumerate($regionsFiles): + #set identifier = re.sub('[^\s\w\-]', '_', str($rf.regionsFile.element_identifier)) + ln -f -s "${rf.regionsFile}" "${identifier}_${counter}.bed" && + #silent $bed_files.append('%s_%s.bed' % ($identifier, $counter)) #end for @BINARY@