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annotate samtools_sort.xml @ 1:cab3f8d35989 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:18:12 -0400
parents a430da4f04cd
children f56bdb93ae58
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cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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1 <tool id="samtools_sort" name="Sort" version="2.0.1">
cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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2 <description>order of storing aligned sequences</description>
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3 <macros>
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cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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4 <import>macros.xml</import>
cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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5 </macros>
cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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6 <expand macro="requirements"/>
cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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7 <expand macro="stdio"/>
cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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8 <expand macro="version_command"/>
cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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9 <command><![CDATA[
cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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10 samtools sort
cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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11 $sort_mode
cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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12 -@ \${GALAXY_SLOTS:-1}
cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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13 -o '${output1}'
cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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14 -O bam
cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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15 -T dataset
cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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16 '${input1}'
cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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17 ]]></command>
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18 <inputs>
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19 <param name="input1" type="data" format="bam" label="BAM File" />
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20 <param name="sort_mode" type="select" label="Sort by ">
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21 <option value="" selected="True">Chromosomal coordinates</option>
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22 <option value="-n">Read names (-n)</option>
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23 </param>
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24 </inputs>
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25 <outputs>
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26 <data name="output1" format="bam" />
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="input1" value="1.bam" ftype="bam" />
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31 <output name="output1" file="1_sort.bam" ftype="bam" sort="True"/>
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32 </test>
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33 <test>
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34 <param name="input1" value="1.bam" ftype="bam" />
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35 <param name="sort_mode" value="-n"/>
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36 <output name="output1" file="1_sort_read_names.bam" ftype="bam" sort="True"/>
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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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42 This tool uses ``samtools sort`` command to sort BAM datasets in coordinate or read name order.
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43 </help>
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cab3f8d35989 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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44 <expand macro="citations"/>
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45 </tool>