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annotate picard_AddCommentsToBam.xml @ 20:2a17c789e0a5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 5ebd6c8453b49dd6a36e372eb1eb6e323bb7ad8a
author iuc
date Tue, 19 Jun 2018 11:28:49 -0400
parents 5053a18d9bc8
children f9242e01365a
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5053a18d9bc8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73
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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 @TMPDIR_OPTION@
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21 VALIDATION_STRINGENCY=${validation_stringency}
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22 ]]></command>
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23
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24 <inputs>
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25 <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />
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26 <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments">
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27 <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/>
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28 </repeat>
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29
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30 <expand macro="VS" />
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31
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32 </inputs>
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34 <outputs>
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35 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with comments"/>
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36 </outputs>
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38
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39 <tests>
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40 <test>
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41 <param name="inputFile" value="picard_AddCommentsToBam.bam" />
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42 <param name="comment" value="test1" />
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43 <param name="validation_stringency" value="LENIENT" />
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44 <output name="outFile" file="picard_AddCommentsToBam_test1.bam" ftype="bam" />
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45 </test>
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46 </tests>
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47 <help>
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48
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49 .. class:: infomark
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50
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51 **Purpose**
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52
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53 Adds one or more comments (@CO) to the header of a specified BAM dataset.
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54
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55 @dataset_collections@
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56
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57 @description@
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58
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59 COMMENT=String
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60 C=String Comments to add to the BAM file This option may be specified 0 or more times.
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62 @more_info@
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63 </help>
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64 <expand macro="citations" />
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65 </tool>