Mercurial > repos > devteam > picard

annotate picard_AddCommentsToBam.xml @ 13:7e6fd3d0f16e draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e
author devteam
date Tue, 06 Dec 2016 10:04:41 -0500
parents 05087b27692a
children 465cbb0cf2eb
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3a3234d7a2e8 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
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1 <tool name="AddCommentsToBam" id="picard_AddCommentsToBam" version="@TOOL_VERSION@.0">
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2 <description>add comments to 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 detect_errors="exit_code"><![CDATA[
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8 @java_options@
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9 @symlink_element_identifier@
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10 picard
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11 AddCommentsToBam
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12 INPUT='$inputFile.element_identifier'
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13 OUTPUT="${outFile}"
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14 #for $element in $comments:
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15 COMMENT="${element.comment}"
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16 #end for
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17 QUIET=true
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18 VERBOSITY=ERROR
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19 VALIDATION_STRINGENCY=${validation_stringency}
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20 ]]></command>
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21
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22 <inputs>
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23 <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
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24 <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments">
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25 <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/>
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26 </repeat>
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27
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28 <expand macro="VS" />
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30 </inputs>
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32 <outputs>
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33 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with comments"/>
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34 </outputs>
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36
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37 <tests>
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38 <test>
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39 <param name="inputFile" value="picard_AddCommentsToBam.bam" />
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40 <param name="comment" value="test1" />
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41 <param name="validation_stringency" value="LENIENT" />
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42 <output name="outFile" file="picard_AddCommentsToBam_test1.bam" ftype="bam" />
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43 </test>
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44 </tests>
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45 <help>
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46
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47 .. class:: infomark
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48
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49 **Purpose**
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50
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51 Adds one or more comments (@CO) to the header of a specified BAM dataset.
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52
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53 @dataset_collections@
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54
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55 @description@
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57 COMMENT=String
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58 C=String Comments to add to the BAM file This option may be specified 0 or more times.
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60 @more_info@
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61 </help>
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62 </tool>
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