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comparison samtools_reheader.xml @ 4:0b97d4e945ab draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:16:51 -0400
parents 77a6694ebf7a
children 747cd1b9ae98
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3:b5e69833722f 4:0b97d4e945ab
1 <tool id="samtools_reheader" name="Reheader" version="2.0"> 1 <tool id="samtools_reheader" name="Reheader" version="2.0.1">
2 <description>copy SAM/BAM header between datasets</description> 2 <description>copy SAM/BAM header between datasets</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"></expand> 6 <expand macro="requirements"/>
7 <expand macro="stdio"></expand> 7 <expand macro="stdio"/>
8 <expand macro="version_command"></expand> 8 <expand macro="version_command"/>
9 <command><![CDATA[samtools reheader "${input_header}" "${input_file}" > "${output}"]]></command> 9 <command><![CDATA[
10 samtools reheader
11 '${input_header}'
12 '${input_file}'
13 > '${output}'
14 ]]></command>
10 <inputs> 15 <inputs>
11 <param name="input_header" type="data" format="sam,bam" label="Select source dataset" help="Header from this dataset will be used to replace header in the target dataset. May be either SAM or BAM dataset."/> 16 <param name="input_header" type="data" format="sam,bam" label="Select source dataset" help="Header from this dataset will be used to replace header in the target dataset. May be either SAM or BAM dataset."/>
12 <param name="input_file" type="data" format="bam" label="Select target dataset" help="Header from the source dataset will be inserted here. Should be a BAM dataset."/> 17 <param name="input_file" type="data" format="bam" label="Select target dataset" help="Header from the source dataset will be inserted here. Should be a BAM dataset."/>
13 </inputs> 18 </inputs>
14 <outputs> 19 <outputs>
16 </outputs> 21 </outputs>
17 <tests> 22 <tests>
18 <test> 23 <test>
19 <param name="input_header" ftype="bam" value="reheader_input_header.bam"/> 24 <param name="input_header" ftype="bam" value="reheader_input_header.bam"/>
20 <param name="input_file" ftype="bam" value="reheader_input_file.bam"/> 25 <param name="input_file" ftype="bam" value="reheader_input_file.bam"/>
21 <output name="output" ftype="bam" file="reheader_out.bam"/> 26 <output name="output" ftype="bam" file="reheader_out.bam" lines_diff="1"/><!-- samtools adds reheader line -->
22 </test> 27 </test>
23 </tests> 28 </tests>
24 <help> 29 <help>
25 **What it does** 30 **What it does**
26 31
27 Copies header from *source* dataset into *target* dataset using ``samtools reheader`` command. 32 Copies header from *source* dataset into *target* dataset using ``samtools reheader`` command.
28
29 </help> 33 </help>
30 <expand macro="citations"></expand> 34 <expand macro="citations"/>
31 </tool> 35 </tool>
32 36