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comparison samtools_split.xml @ 7:b6caca6a4ca5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:23:35 +0000
parents eda9f7aa1d54
children
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6:eda9f7aa1d54 7:b6caca6a4ca5
1 <tool id="samtools_split" name="Samtools split" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 1 <tool id="samtools_split" name="Samtools split" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>BAM dataset on readgroups</description> 2 <description>BAM dataset on readgroups</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @ADDTHREADS@ 10 @ADDTHREADS@
11 samtools split -f 'Read_Group_%!.bam' 11 samtools split -f 'Read_Group_%!.bam' --output-fmt 'bam'
12 #if $header: 12 #if $header:
13 -u '${output}:${header}' 13 -h $header'
14 #else:
15 -u '${output}'
16 #end if 14 #end if
15 -u '$output'
17 -@ \$addthreads 16 -@ \$addthreads
18 '$input_bam' 17 '$input_bam'
19 ]]></command> 18 ]]></command>
20 <inputs> 19 <inputs>
21 <param name="input_bam" type="data" format="bam" label="BAM file" /> 20 <param name="input_bam" type="data" format="bam" label="BAM file" />
39 <help><![CDATA[ 38 <help><![CDATA[
40 **What it does** 39 **What it does**
41 40
42 Splits BAM files on readgroups. 41 Splits BAM files on readgroups.
43 42
44 This tool is based on ``samtools split`` command. It will generate multiple output datasets for each redagroup from the input dataset. 43 This tool is based on ``samtools split`` command. It will generate multiple output datasets for each readgroup from the input dataset.
45 ]]></help> 44 ]]></help>
46 <expand macro="citations"/> 45 <expand macro="citations"/>
47 </tool> 46 </tool>