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comparison picard_CollectRnaSeqMetrics.xml @ 22:f6ced08779c4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit b6e11aa8e5fd1da27909207ec4f09cbbac467495
author iuc
date Fri, 29 Mar 2019 08:34:36 -0400
parents 2a17c789e0a5
children a1f0b3f4b781
comparison
equal deleted inserted replaced
21:6f9c0884a3e7 22:f6ced08779c4
21 ## refFlat data 21 ## refFlat data
22 ## The awk line below converts a file obtained from UCSC as specified in the tool help to refFlat format 22 ## The awk line below converts a file obtained from UCSC as specified in the tool help to refFlat format
23 23
24 #if str($gene_reference_source.gene_reference_source_selector) == "gtf" 24 #if str($gene_reference_source.gene_reference_source_selector) == "gtf"
25 #if $gene_reference_source.refFlat.ext != 'gff3' 25 #if $gene_reference_source.refFlat.ext != 'gff3'
26 gtfToGenePred '${gene_reference_source.refFlat}' refFlat.tab.raw && 26 gtfToGenePred -genePredExt '${gene_reference_source.refFlat}' refFlat.tab.raw &&
27 #else 27 #else
28 gff3ToGenePred '${gene_reference_source.refFlat}' refFlat.tab.raw && 28 gff3ToGenePred '${gene_reference_source.refFlat}' refFlat.tab.raw &&
29 #end if 29 #end if
30 30
31 grep -v '^#' refFlat.tab.raw | awk '{print $12"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10}' > refFlat.tab && 31 grep -v '^#' refFlat.tab.raw | awk '{print $12"\t"$1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10}' > refFlat.tab &&