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1 <tool id="picard_SortSam" name="SortSam" version="1.135">
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2 <description>sort SAM/BAM dataset</description>
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3 <macros>
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4 <import>picard_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command>
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8 @java_options@
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9 java -jar \$JAVA_JAR_PATH/picard.jar
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10 SortSam
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11 INPUT="${inputFile}"
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12 OUTPUT="${outFile}"
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13 SORT_ORDER="${sort_order}"
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14 QUIET=true
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15 VERBOSITY=ERROR
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16 VALIDATION_STRINGENCY=${validation_stringency}
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17 </command>
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18
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19 <inputs>
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20 <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
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21 <param name="sort_order" type="select" display="radio" label="Sort order" help="SORT_ORDER; default=coordinate">
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22 <option value="coordinate" selected="True">Coordinate</option>
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23 <option value="queryname">Queryname</option>
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24 <option value="unsorted">Unsorted</option>
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25 </param>
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26 <expand macro="VS" />
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27 </inputs>
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28
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29 <outputs>
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30 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM sorted in ${sort_order} order">
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31 </data>
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32 </outputs>
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33
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34 <stdio>
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35 <exit_code range="1:" level="fatal"/>
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36 </stdio>
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37
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38 <tests>
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39 <test>
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40 <param name="inputFile" ftype="bam" value="picard_SortSam.bam" />
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41 <param name="sort_order" value="queryname"/>
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42 <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="2"/>
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43 </test>
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44 </tests>
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45
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46 <help>
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47
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48 .. class:: infomark
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49
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50 **Purpose**
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51
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52 Sorts the input SAM or BAM.
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53
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54 @dataset_collections@
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55
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56 @description@
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57
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58 SORT_ORDER=SortOrder
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59 SO=SortOrder Sort order of output file Required. Possible values: {unsorted, queryname, coordinate}
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60
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61 @more_info@
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62
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63 </help>
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64 </tool>
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