Mercurial > repos > nilesh > rseqc

diff bam2wig.xml @ 60:1421603cc95b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
author iuc
date Sat, 26 Nov 2022 15:19:14 +0000
parents dbedfc5f5a3c
children 5968573462fa
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--- a/bam2wig.xml	Sat Dec 18 19:41:19 2021 +0000
+++ b/bam2wig.xml	Sat Nov 26 15:19:14 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="rseqc_bam2wig" name="BAM to Wiggle" version="@TOOL_VERSION@">
+<tool id="rseqc_bam2wig" name="BAM to Wiggle" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>
         converts all types of RNA-seq data from .bam to .wig
     </description>
@@ -14,9 +14,8 @@
     <version_command><![CDATA[bam2wig.py --version]]></version_command>
 
     <command><![CDATA[
-        ln -sf '${input}' 'input.bam' &&
-        ln -sf '${input.metadata.bam_index}' 'input.bam.bai' &&
-        bam2wig.py -i 'input.bam' -s '${chromsize}' -o outfile
+        @BAM_SAM_INPUTS@
+        bam2wig.py -i 'input.${extension}' -s '${chromsize}' -o outfile
 
         #if str($strand_type.strand_specific) == "pair"
             -d