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annotate 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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0b97d4e945ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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1 <tool id="samtools_reheader" name="Reheader" version="2.0.1">
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2 <description>copy SAM/BAM header between datasets</description>
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3 <macros>
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iuc
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4 <import>macros.xml</import>
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iuc
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5 </macros>
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iuc
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6 <expand macro="requirements"/>
0b97d4e945ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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7 <expand macro="stdio"/>
0b97d4e945ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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8 <expand macro="version_command"/>
0b97d4e945ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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9 <command><![CDATA[
0b97d4e945ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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10 samtools reheader
0b97d4e945ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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11 '${input_header}'
0b97d4e945ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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12 '${input_file}'
0b97d4e945ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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13 > '${output}'
0b97d4e945ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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14 ]]></command>
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15 <inputs>
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16 <param name="input_header" type="data" format="sam,bam" label="Select source dataset" help="Header from this dataset will be used to replace header in the target dataset. May be either SAM or BAM dataset."/>
77a6694ebf7a planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
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17 <param name="input_file" type="data" format="bam" label="Select target dataset" help="Header from the source dataset will be inserted here. Should be a BAM dataset."/>
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18 </inputs>
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19 <outputs>
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20 <data format="bam" name="output" label="${tool.name} on ${on_string}" />
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="input_header" ftype="bam" value="reheader_input_header.bam"/>
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25 <param name="input_file" ftype="bam" value="reheader_input_file.bam"/>
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0b97d4e945ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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26 <output name="output" ftype="bam" file="reheader_out.bam" lines_diff="1"/><!-- samtools adds reheader line -->
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27 </test>
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28 </tests>
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29 <help>
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30 **What it does**
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31
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32 Copies header from *source* dataset into *target* dataset using ``samtools reheader`` command.
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33 </help>
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0b97d4e945ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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34 <expand macro="citations"/>
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35 </tool>
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36