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comparison samblaster.xml @ 3:595c942ad3ad draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/samblaster commit 32feb54c292e406e2982f92284fb7ba1f0401e5b
author iuc
date Mon, 07 Oct 2024 06:45:22 +0000
parents c07ffa5e508d
children
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2:c07ffa5e508d 3:595c942ad3ad
1 <tool id="samblaster" name="samblaster" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1"> 1 <tool id="samblaster" name="samblaster" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1">
2 <description>marks duplicates, outputs split reads, discordant read pairs and unmapped reads</description> 2 <description>marks duplicates, outputs split reads, discordant read pairs and unmapped reads</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">0.1.24</token> 4 <token name="@TOOL_VERSION@">0.1.26</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros> 6 </macros>
7 <xrefs> 7 <xrefs>
8 <xref type="bio.tools">samblaster</xref> 8 <xref type="bio.tools">samblaster</xref>
9 </xrefs> 9 </xrefs>
10 <requirements> 10 <requirements>
11 <requirement type="package" version="@TOOL_VERSION@">samblaster</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">samblaster</requirement>
12 <requirement type="package" version="0.6.5">sambamba</requirement> 12 <requirement type="package" version="1.0.1">sambamba</requirement>
13 </requirements> 13 </requirements>
14 <version_command>samblaster --version</version_command> 14 <version_command>samblaster --version</version_command>
15 <command detect_errors="exit_code"><![CDATA[ 15 <command detect_errors="exit_code"><![CDATA[
16 #if $input.is_of_type('sam'): 16 #if $input.is_of_type('sam'):
17 #set stream="<(sambamba view -S -f bam -t ${GALAXY_SLOTS:-4} -h '%s')" % $input 17 #set stream="<(sambamba view -S -f bam -t ${GALAXY_SLOTS:-4} -h '%s')" % $input