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1 <tool name="Sort Sam" id="picard_SortSam" version="1.106.0">
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2 <!-- adapted from https://github.com/najoshi/ucd-biocore-galaxy/blob/master/tools/picard/picard_SortSam.xml -->
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3 <!-- warning: the sam format output doesn't work. TODO: fix it -->
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4 <description>Sorts SAM or BAM file</description>
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5 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
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6 <command interpreter="python">
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7 picard_wrapper.py
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8 --input "$inputFile"
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9 -s "$sort_order"
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10 -o "$outFile"
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11 --output-format $outputFormat
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12 -j "\$JAVA_JAR_PATH/SortSam.jar"
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13 </command>
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14 <inputs>
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15 <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be sorted"
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16 help="If empty, upload or import a SAM/BAM dataset." />
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17 <param name="sort_order" type="select" label="Sort order">
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18 <option value="coordinate" selected="True">coordinate</option>
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19 <option value="queryname">queryname</option>
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20 <option value="unsorted">unsorted</option>
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21 </param>
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22 <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
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23 </inputs>
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24 <outputs>
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25 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: ${outputFormat}" />
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26 <change_format>
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27 <when input="outputFormat" value="sam" format="sam" />
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28 </change_format>
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29 </outputs>
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30 <help>
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31
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32 SortSam
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33
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34 USAGE: SortSam [options]
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35
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36 Documentation: http://picard.sourceforge.net/command-line-overview.shtml#SortSam
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37
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38 Sorts the input SAM or BAM.
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39
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40 Input and output formats are determined by file extension.
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41 Option Description
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42 INPUT=File The BAM or SAM file to sort. Required.
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43 OUTPUT=File The sorted BAM or SAM output file. Required.
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44 SORT_ORDER=SortOrder Sort order of output file Required. Possible values: {unsorted, queryname, coordinate}
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45 </help>
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46 </tool>
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47
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48
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49
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