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annotate picard_AddCommentsToBam.xml @ 32:f9242e01365a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 285fab1660daa944d6833ae1e059b30cb1e88309
author iuc
date Mon, 25 Sep 2023 08:32:17 +0000
parents 2a17c789e0a5
children 3f254c5ced1d
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1 <tool name="AddCommentsToBam" id="picard_AddCommentsToBam" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
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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 <token name="@WRAPPER_VERSION@">1</token>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 @java_options@
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10 @symlink_element_identifier@
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11 picard
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12 AddCommentsToBam
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13 INPUT='$escaped_element_identifier'
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14 OUTPUT="${outFile}"
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15 #for $element in $comments:
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16 COMMENT="${element.comment}"
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17 #end for
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18 QUIET=true
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19 VERBOSITY=ERROR
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20 VALIDATION_STRINGENCY=${validation_stringency}
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21 ]]></command>
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22
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23 <inputs>
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24 <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
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25 <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments">
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26 <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/>
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27 </repeat>
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28
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29 <expand macro="VS" />
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30
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31 </inputs>
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32
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33 <outputs>
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34 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with comments"/>
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35 </outputs>
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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" value="picard_AddCommentsToBam.bam" />
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41 <param name="comment" value="test1" />
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42 <param name="validation_stringency" value="LENIENT" />
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43 <output name="outFile" file="picard_AddCommentsToBam_test1.bam" ftype="bam" />
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44 </test>
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45 </tests>
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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 Adds one or more comments (@CO) to the header of a specified BAM dataset.
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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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58 COMMENT=String
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59 C=String Comments to add to the BAM file This option may be specified 0 or more times.
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61 @more_info@
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62 </help>
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63 <expand macro="citations" />
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64 </tool>