Mercurial > repos > nilesh > rseqc
diff geneBody_coverage.xml @ 57:f437057e46f1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 7d7cd4324af66710b89801a1a1c79fb8abf0d146
| author | iuc |
|---|---|
| date | Thu, 27 Sep 2018 14:23:52 -0400 |
| parents | b0b62dcd0a35 |
| children | dbedfc5f5a3c |
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--- a/geneBody_coverage.xml Tue Sep 18 09:11:06 2018 -0400 +++ b/geneBody_coverage.xml Thu Sep 27 14:23:52 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="rseqc_geneBody_coverage" name="Gene Body Coverage (BAM)" version="@WRAPPER_VERSION@.2"> +<tool id="rseqc_geneBody_coverage" name="Gene Body Coverage (BAM)" version="@WRAPPER_VERSION@.3"> <description> Read coverage over gene body. </description> @@ -29,9 +29,9 @@ #end for geneBody_coverage.py -i 'input_list.txt' -r '${refgene}' --minimum_length ${minimum_length} -o output #else - #set $safename = re.sub('[^\w\-_]', '_', $input.element_identifier) - ln -sf '${input}' '${safename}.bam' && - ln -sf '${input.metadata.bam_index}' '${safename}.bam.bai' && + #set $safename = re.sub('[^\w\-_]', '_', $batch_mode.input.element_identifier) + ln -sf '${batch_mode.input}' '${safename}.bam' && + ln -sf '${batch_mode.input.metadata.bam_index}' '${safename}.bam.bai' && geneBody_coverage.py -i '${safename}.bam' -r '${refgene}' --minimum_length ${minimum_length} -o output #end if ]]>