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comparison bamtools_split.xml @ 4:0a7b0989fa09 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_split commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a"
author iuc
date Sat, 27 Nov 2021 10:04:19 +0000
parents 9676127a1ed2
children
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3:9676127a1ed2 4:0a7b0989fa09
1 <tool id="bamtools_split" name="Split" version="2.4.0"> 1 <tool id="bamtools_split" name="Split" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>BAM datasets on variety of attributes</description> 2 <description>BAM datasets on variety of attributes</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="2.4.0">bamtools</requirement> 4 <import>macros.xml</import>
5 </requirements> 5 </macros>
6 <expand macro="requirements"/>
6 <command> 7 <command>
7 <![CDATA[ 8 <![CDATA[
8 echo "BAM" > $report && 9 echo "BAM" > $report &&
9 #for $bam_count, $input_bam in enumerate( $input_bams ): 10 #for $bam_count, $input_bam in enumerate( $input_bams ):
10 ln -s "${input_bam}" "localbam_${bam_count}.bam" && 11 ln -s "${input_bam}" "localbam_${bam_count}.bam" &&
57 </output> 58 </output>
58 </test> 59 </test>
59 <test> 60 <test>
60 <param name="input_bams" ftype="bam" value="bamtools-input2.bam"/> 61 <param name="input_bams" ftype="bam" value="bamtools-input2.bam"/>
61 <param name="analysis_type_selector" value="-reference"/> 62 <param name="analysis_type_selector" value="-reference"/>
62 <param name="output_type" value="dataset_collection"/>
63 <output name="report"> 63 <output name="report">
64 <assert_contents> 64 <assert_contents>
65 <has_line line="BAM" /> 65 <has_line line="BAM" />
66 </assert_contents> 66 </assert_contents>
67 <discovered_dataset designation="REF_chr1" file="bamtools_input2.chr1" ftype="bam"/> 67 <discovered_dataset designation="REF_chr1" file="bamtools_input2.chr1" ftype="bam"/>