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annotate samtools_split.xml @ 2:135c85f4cfaf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
author iuc
date Mon, 29 Jul 2019 08:49:33 -0400
parents b7f7826ef1cd
children 5d9ae78f34d3
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b7f7826ef1cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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1 <tool id="samtools_split" name="Split" version="@TOOL_VERSION@">
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2 <description>BAM dataset on readgroups</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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b7f7826ef1cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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6 <expand macro="requirements"/>
b7f7826ef1cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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7 <expand macro="stdio"/>
b7f7826ef1cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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135c85f4cfaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
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10 @ADDTHREADS@
135c85f4cfaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
iuc
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11 samtools split -f 'Read_Group_%!.bam'
135c85f4cfaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
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12 #if $header:
135c85f4cfaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
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13 -u '${output}:${header}'
135c85f4cfaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
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14 #else:
135c85f4cfaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
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15 -u '${output}'
135c85f4cfaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
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16 #end if
135c85f4cfaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
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17 -@ \$addthreads
135c85f4cfaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
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18 '$input_bam'
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b7f7826ef1cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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19 ]]></command>
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20 <inputs>
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21 <param name="input_bam" type="data" format="bam" label="BAM file" />
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b7f7826ef1cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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22 <param name="header" type="data" format="bam,sam" optional="True" label="Replace header in output file" />
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23 </inputs>
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24 <outputs>
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b7f7826ef1cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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25 <data name="output" format="bam" label="${tool.name} on ${on_string}">
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135c85f4cfaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
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26 <discover_datasets pattern="Read_Group_(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="true" directory="" assign_primary_output="false"/>
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27 </data>
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="input_bam" value="phiX.bam" ftype="bam" />
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135c85f4cfaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit ca0d1d44099fd21e0f8214102f4d8a2fd2d054d6
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32 <output name="output">
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33 <discovered_dataset designation="Mouse" ftype="bam" file="phiX_Mouse.bam" />
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34 <discovered_dataset designation="Elephant" ftype="bam" file="phiX_Elephant.bam" />
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35 <discovered_dataset designation="Human" ftype="bam" file="phiX_Human.bam" />
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36 </output>
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37 </test>
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38 </tests>
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b7f7826ef1cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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39 <help><![CDATA[
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40 **What it does**
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41
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42 Splits BAM files on readgroups.
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43
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b7f7826ef1cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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44 This tool is based on ``samtools split`` command. It will generate multiple output datasets for each redagroup from the input dataset.
b7f7826ef1cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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45 ]]></help>
b7f7826ef1cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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46 <expand macro="citations"/>
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47 </tool>