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1 <tool id="samtools_sort" name="Sort" version="2.0">
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2 <description>BAM dataset</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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6 <expand macro="requirements"></expand>
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7 <expand macro="stdio"></expand>
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8 <expand macro="version_command"></expand>
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9 <command>samtools sort $sort_mode -@ \${GALAXY_SLOTS:-1} -o "${output1}" -O bam -T dataset "${input1}"</command>
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10 <inputs>
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11 <param name="input1" type="data" format="bam" label="BAM File" />
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12 <param name="sort_mode" type="select" label="Sort by ">
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13 <option value="" selected="True">Chromosomal coordinates</option>
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14 <option value="-n">Read names (-n)</option>
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15 </param>
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16 </inputs>
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17 <outputs>
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18 <data name="output1" format="bam" />
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19 </outputs>
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20 <tests>
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21 <test>
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22 <param name="input1" value="1.bam" ftype="bam" />
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23 <output name="output1" file="1_sort.bam" ftype="bam" sort="True"/>
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24 </test>
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25 <test>
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26 <param name="input1" value="1.bam" ftype="bam" />
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27 <param name="sort_mode" value="-n"/>
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28 <output name="output1" file="1_sort_read_names.bam" ftype="bam" sort="True"/>
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29 </test>
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30 </tests>
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31 <help>
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32
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33 **What it does**
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34
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35 This tool uses ``samtools sort`` command to sort BAM datasets in coordinate or read name order.
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36
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37
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38 </help>
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39 <expand macro="citations"></expand>
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40 </tool>
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