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annotate picard_SortSam.xml @ 5:2f3cdd537834 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 6e148b31fed1b322ce720804d8525088ec6d43f9
author devteam
date Thu, 29 Oct 2015 22:23:28 -0400
parents 52fdfc45590a
children 08f69add4d06
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2f3cdd537834 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 6e148b31fed1b322ce720804d8525088ec6d43f9
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1 <tool id="picard_SortSam" name="SortSam" version="@TOOL_VERSION@.1">
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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 </param>
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25 <expand macro="VS" />
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26 </inputs>
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28 <outputs>
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29 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM sorted in ${sort_order} order">
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30 </data>
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31 </outputs>
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33 <stdio>
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34 <exit_code range="1:" level="fatal"/>
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35 </stdio>
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37 <tests>
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38 <test>
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39 <param name="inputFile" ftype="bam" value="picard_SortSam.bam" />
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40 <param name="sort_order" value="queryname"/>
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41 <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="2"/>
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42 </test>
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43 </tests>
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45 <help>
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47 .. class:: infomark
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49 **Purpose**
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51 Sorts the input SAM or BAM.
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52
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53 @dataset_collections@
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55 @description@
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57 SORT_ORDER=SortOrder
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58 SO=SortOrder Sort order of output file. You can either sort by queryname or by coordinate.
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60 @more_info@
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62 </help>
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63 </tool>