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comparison samtools_idxstats.xml @ 2:04d5581db1f5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_idxstats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
author iuc
date Thu, 27 Sep 2018 09:03:08 -0400
parents 88b8c2916784
children 811fc2d75ad4
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1:88b8c2916784 2:04d5581db1f5
1 <tool id="samtools_idxstats" name="IdxStats" version="2.0.1"> 1 <tool id="samtools_idxstats" name="Samtools idxstats" version="2.0.2">
2 <description>reports stats of the BAM index file</description> 2 <description>reports stats of the BAM index file</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 ln -f -s '${input.metadata.bam_index}' '${input}.bai' && 10 @PREPARE_IDX@
11 11 samtools idxstats infile > '${output}'
12 samtools idxstats '${input}' > '${output}'
13 ]]></command> 12 ]]></command>
14 <inputs> 13 <inputs>
15 <param name="input" type="data" format="bam" label="BAM file" /> 14 <param name="input" type="data" format="bam,cram" label="BAM file" />
16 </inputs> 15 </inputs>
17 <outputs> 16 <outputs>
18 <data format="tabular" name="output" label="${tool.name} on ${on_string}" /> 17 <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
19 </outputs> 18 </outputs>
20 <tests> 19 <tests>
20 <!-- test from https://github.com/samtools/samtools/blob/9ce8c64493f7ea3fa69bc5c1ac980b1a8e3dcf1f/test/test.pl#L2556 -->
21 <test> 21 <test>
22 <param name="input" value="test_input_1_a.bam" ftype="bam" />
23 <output name="output" file="test_input_1_a.bam.expected" compare="diff" ftype="tabular" />
24 </test>
25 <!-- test from original tool -->
26 <test>
22 <param name="input" value="phiX.bam" ftype="bam" /> 27 <param name="input" value="phiX.bam" ftype="bam" />
23 <output name="output" file="samtools_idxstats_out.tabular" compare="diff" ftype="tabular" /> 28 <output name="output" file="samtools_idxstats_out.tabular" compare="diff" ftype="tabular" />
24 </test> 29 </test>
25 </tests> 30 </tests>
26 <help><![CDATA[ 31 <help><![CDATA[