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comparison RNA_fragment_size.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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59:dbedfc5f5a3c 60:1421603cc95b
1 <tool id="rseqc_RNA_fragment_size" name="RNA fragment size" version="@TOOL_VERSION@.1"> 1 <tool id="rseqc_RNA_fragment_size" name="RNA fragment size" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
2 <description> 2 <description>
3 calculates the fragment size for each gene/transcript 3 calculates the fragment size for each gene/transcript
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[RNA_fragment_size.py --version]]></version_command> 14 <version_command><![CDATA[RNA_fragment_size.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 RNA_fragment_size.py -i 'input.${extension}' --refgene='${refgene}' --mapq=${mapq} --frag-num=${fragnum} > '${output}'
19 RNA_fragment_size.py -i 'input.bam' --refgene='${refgene}' --mapq=${mapq} --frag-num=${fragnum} > '${output}'
20 ]]> 19 ]]>
21 </command> 20 </command>
22 21
23 <inputs> 22 <inputs>
24 <expand macro="bam_param" /> 23 <expand macro="bam_param" />