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1 <tool id="samtools_sort" name="sort" version="1.0.3">
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3
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2 <requirements>
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4
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3 <requirement type="package" version="1.1">samtools</requirement>
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3
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4 </requirements>
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5 <description>a BAM file</description>
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5
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6 <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
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7 <command>samtools sort $sort_mode "${input1}" -o "${output1}" -O bam -T dataset</command>
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8 <stdio>
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9 <exit_code range="1:" level="fatal" description="Error" />
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10 </stdio>
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3
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11 <inputs>
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12 <param name="input1" type="data" format="bam" label="BAM File" />
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13 <param name="sort_mode" type="select" label="Sort by ">
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14 <option value="" selected="True">Chromosomal coordinates</option>
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15 <option value="-n">Read names</option>
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16 </param>
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17 </inputs>
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18 <outputs>
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19 <data name="output1" format="bam" />
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="input1" value="1.bam" ftype="bam" />
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24 <output name="output1" file="1_sort.bam" ftype="bam" sort="True"/>
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25 </test>
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26 </tests>
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27 <help>
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28
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29 **What it does**
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30
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31 This tool uses the SAMTools_ toolkit to sort alignments by leftmost coordinates or read names.
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32
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33 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
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34
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35 ------
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36
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37 **Citation**
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38
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39 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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40
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41 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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42
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43 </help>
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44 </tool>
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