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comparison geneBody_coverage.xml @ 57:f437057e46f1 draft

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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
comparison
equal deleted inserted replaced
56:daae0a118c36 57:f437057e46f1
1 <tool id="rseqc_geneBody_coverage" name="Gene Body Coverage (BAM)" version="@WRAPPER_VERSION@.2"> 1 <tool id="rseqc_geneBody_coverage" name="Gene Body Coverage (BAM)" version="@WRAPPER_VERSION@.3">
2 <description> 2 <description>
3 Read coverage over gene body. 3 Read coverage over gene body.
4 </description> 4 </description>
5 5
6 <macros> 6 <macros>
27 ln -sf '${input.metadata.bam_index}' '${safename}.bam.bai' && 27 ln -sf '${input.metadata.bam_index}' '${safename}.bam.bai' &&
28 echo '${safename}.bam' >> 'input_list.txt' && 28 echo '${safename}.bam' >> 'input_list.txt' &&
29 #end for 29 #end for
30 geneBody_coverage.py -i 'input_list.txt' -r '${refgene}' --minimum_length ${minimum_length} -o output 30 geneBody_coverage.py -i 'input_list.txt' -r '${refgene}' --minimum_length ${minimum_length} -o output
31 #else 31 #else
32 #set $safename = re.sub('[^\w\-_]', '_', $input.element_identifier) 32 #set $safename = re.sub('[^\w\-_]', '_', $batch_mode.input.element_identifier)
33 ln -sf '${input}' '${safename}.bam' && 33 ln -sf '${batch_mode.input}' '${safename}.bam' &&
34 ln -sf '${input.metadata.bam_index}' '${safename}.bam.bai' && 34 ln -sf '${batch_mode.input.metadata.bam_index}' '${safename}.bam.bai' &&
35 geneBody_coverage.py -i '${safename}.bam' -r '${refgene}' --minimum_length ${minimum_length} -o output 35 geneBody_coverage.py -i '${safename}.bam' -r '${refgene}' --minimum_length ${minimum_length} -o output
36 #end if 36 #end if
37 ]]> 37 ]]>
38 </command> 38 </command>
39 39