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1 <tool id="samtools_split" name="Split" version="1.1">
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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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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><![CDATA[
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10 samtools split -f 'Read_Group_%!.bam'
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11 #if $header:
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12 -u "${output}":"${header}"
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13 #else:
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14 -u "${output}"
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15 #end if
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16 "${input_bam}"
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17 ]]></command>
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18 <inputs>
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19 <param name="input_bam" type="data" format="bam" label="BAM file" />
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20 <param name="header" type="data" format="bam,sam" label="Replace header in output file" optional="True" />
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21 </inputs>
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22 <outputs>
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23 <data format="bam" name="output" label="${tool.name} on ${on_string}">
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24 <discover_datasets pattern="Read_Group_(?P<designation>.+)\.bam" ext="bam" visible="true" directory="" />
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25 </data>
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="input_bam" value="phiX.bam" ftype="bam" />
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30 <output name="output" file="samtools_split_out.bam">
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31 <discovered_dataset designation="Mouse" ftype="bam" file="phiX_Mouse.bam" />
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32 <discovered_dataset designation="Elephant" ftype="bam" file="phiX_Elephant.bam" />
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33 <discovered_dataset designation="Human" ftype="bam" file="phiX_Human.bam" />
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34 </output>
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35 </test>
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36 </tests>
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37 <help>
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38 **What it does**
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39
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40 Splits BAM files on readgroups.
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41
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42 This tool is based on ``samtools split`` command. It will generate multiple output datasets for each redagroup from the input dataset.
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43
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44 </help>
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45 <expand macro="citations"></expand>
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46 </tool>
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47
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