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1 <tool id="samtools_split" name="Split" version="1.0.0">
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2 <description>a BAM file by read group</description>
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3 <requirements>
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4 <requirement type="package" version="1.1">samtools</requirement>
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5 </requirements>
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6 <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
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7 <command><![CDATA[
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8 samtools split -f 'Read_Group_%!.bam'
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9 #if $header:
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10 -u "${output}":"${header}"
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11 #else:
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12 -u "${output}"
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13 #end if
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14 "${input_bam}"
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15 ]]></command>
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16 <stdio>
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17 <exit_code range="1:" level="fatal" description="Error" />
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18 </stdio>
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19 <inputs>
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20 <param name="input_bam" type="data" format="bam" label="BAM file" multiple="true" />
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21 <param name="header" type="data" format="bam,sam" label="Replace header in output file" optional="True" />
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22 </inputs>
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23 <outputs>
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24 <data format="bam" name="output" label="${tool.name} on ${on_string}">
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25 <discover_datasets pattern="Read_Group_(?P<designation>.+)\.bam" ext="bam" visible="true" directory="" />
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26 </data>
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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="input_bam" value="phiX.bam" ftype="bam" />
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31 <output name="output" file="samtools_split_out.bam">
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32 <discovered_dataset designation="Mouse" ftype="bam" file="phiX_Mouse.bam" />
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33 <discovered_dataset designation="Elephant" ftype="bam" file="phiX_Elephant.bam" />
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34 <discovered_dataset designation="Human" ftype="bam" file="phiX_Human.bam" />
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35 </output>
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36 </test>
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37 </tests>
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38 <help>
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39 **What it does**
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40
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41 This tool runs the ``samtools split`` command in the SAMtools toolkit.
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42
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43 Split BAM files by read group.
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44
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45 **Citation**
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46
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47 For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_
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48
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49
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50 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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51 </help>
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52 </tool>
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53
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