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comparison 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
comparison
equal deleted inserted replaced
59:dbedfc5f5a3c 60:1421603cc95b
1 <tool id="rseqc_bam2wig" name="BAM to Wiggle" version="@TOOL_VERSION@"> 1 <tool id="rseqc_bam2wig" name="BAM to Wiggle" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
2 <description> 2 <description>
3 converts all types of RNA-seq data from .bam to .wig 3 converts all types of RNA-seq data from .bam to .wig
4 </description> 4 </description>
5 <expand macro="bio_tools"/> 5 <expand macro="bio_tools"/>
6 <macros> 6 <macros>
12 <expand macro="stdio" /> 12 <expand macro="stdio" />
13 13
14 <version_command><![CDATA[bam2wig.py --version]]></version_command> 14 <version_command><![CDATA[bam2wig.py --version]]></version_command>
15 15
16 <command><![CDATA[ 16 <command><![CDATA[
17 ln -sf '${input}' 'input.bam' && 17 @BAM_SAM_INPUTS@
18 ln -sf '${input.metadata.bam_index}' 'input.bam.bai' && 18 bam2wig.py -i 'input.${extension}' -s '${chromsize}' -o outfile
19 bam2wig.py -i 'input.bam' -s '${chromsize}' -o outfile
20 19
21 #if str($strand_type.strand_specific) == "pair" 20 #if str($strand_type.strand_specific) == "pair"
22 -d 21 -d
23 #if str($strand_type.pair_type) == "sd" 22 #if str($strand_type.pair_type) == "sd"
24 '1++,1--,2+-,2-+' 23 '1++,1--,2+-,2-+'