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annotate samtools_reheader.xml @ 6:747cd1b9ae98 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
author iuc
date Mon, 06 Jul 2020 18:13:42 +0000
parents 0b97d4e945ab
children 71db7f3a33b9
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747cd1b9ae98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
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1 <tool id="samtools_reheader" name="Reheader" version="2.0.1+galaxy1">
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2 <description>copy SAM/BAM header between datasets</description>
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3 <macros>
4
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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>
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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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"/>
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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
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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
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11 '${input_header}'
0b97d4e945ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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12 '${input_file}'
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747cd1b9ae98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
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13 ${no_pg}
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14 > '${output}'
0b97d4e945ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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15 ]]></command>
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16 <inputs>
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17 <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."/>
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18 <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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747cd1b9ae98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
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19 <param argument="--no-PG" name="no_pg" type="boolean" truevalue="--no-PG" falsevalue=""
747cd1b9ae98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
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20 label="Keep the new header unmodified?"
747cd1b9ae98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
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21 help="By default, samtools reheader will add itself to the chain of tools used to manipulate the target dataset, which will cause one or more @PG records to be inserted into the new header. If you want the output dataset to end up with the header of the source dataset exactly, you should activate this option." />
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22 </inputs>
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23 <outputs>
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24 <data format="bam" name="output" label="${tool.name} on ${on_string}" />
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="input_header" ftype="bam" value="reheader_input_header.bam"/>
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29 <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
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30 <output name="output" ftype="bam" file="reheader_out.bam" lines_diff="1"/><!-- samtools adds reheader line -->
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31 </test>
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747cd1b9ae98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
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32 <test>
747cd1b9ae98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
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33 <param name="input_header" ftype="bam" value="reheader_input_header.bam"/>
747cd1b9ae98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
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34 <param name="input_file" ftype="bam" value="reheader_input_file.bam"/>
747cd1b9ae98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
iuc
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35 <param name="no_pg" value="true"/>
747cd1b9ae98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
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36 <output name="output" ftype="bam" file="reheader_out.bam" />
747cd1b9ae98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
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37 </test>
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38 </tests>
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39 <help>
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40 **What it does**
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41
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747cd1b9ae98 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_reheader commit f667915d861dbf0a25cc8fd132cc956d82e73ee9"
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42 Generates a new BAM dataset with the contents of *target* dataset, but the header of *source* dataset using the ``samtools reheader`` command.
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43 </help>
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44 <expand macro="citations"/>
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45 </tool>
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46