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comparison picard_AddCommentsToBam.xml @ 33:3f254c5ced1d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8
author iuc
date Sun, 03 Mar 2024 16:06:11 +0000
parents f9242e01365a
children
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equal deleted inserted replaced
32:f9242e01365a 33:3f254c5ced1d
1 <tool name="AddCommentsToBam" id="picard_AddCommentsToBam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="AddCommentsToBam" id="picard_AddCommentsToBam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
2 <description>add comments to BAM dataset</description> 2 <description>add comments to BAM dataset</description>
3 <macros> 3 <macros>
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 <token name="@WRAPPER_VERSION@">1</token> 5 <token name="@WRAPPER_VERSION@">0</token>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 @java_options@ 9 @java_options@
10 @symlink_element_identifier@ 10 ## linking does not work, picard complains about not writable file. Hopefully this can be removed in future version.
11 ##@symlink_element_identifier@
12 #import re
13 #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
14 cp '$inputFile' '$escaped_element_identifier' &&
15
11 picard 16 picard
12 AddCommentsToBam 17 AddCommentsToBam
13 INPUT='$escaped_element_identifier' 18 --INPUT '$escaped_element_identifier'
14 OUTPUT="${outFile}" 19 --OUTPUT '${outFile}'
15 #for $element in $comments: 20 #for $element in $comments:
16 COMMENT="${element.comment}" 21 --COMMENT '${element.comment}'
17 #end for 22 #end for
18 QUIET=true 23 --QUIET true
19 VERBOSITY=ERROR 24 --VERBOSITY ERROR
20 VALIDATION_STRINGENCY=${validation_stringency} 25 --VALIDATION_STRINGENCY ${validation_stringency}
21 ]]></command> 26 ]]></command>
22 27 <inputs>
23 <inputs> 28 <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
24 <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" /> 29 <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments">
25 <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments"> 30 <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/>
26 <param name="comment" type="text" label="Add this comment to BAM dataset" help="COMMENT"/> 31 </repeat>
27 </repeat> 32 <expand macro="VS"/>
28 33 </inputs>
29 <expand macro="VS" /> 34 <outputs>
30 35 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with comments"/>
31 </inputs> 36 </outputs>
32 37 <tests>
33 <outputs> 38 <test>
34 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with comments"/> 39 <param name="inputFile" value="picard_AddCommentsToBam.bam"/>
35 </outputs> 40 <param name="comment" value="test1"/>
36 41 <param name="validation_stringency" value="LENIENT"/>
37 42 <output name="outFile" file="picard_AddCommentsToBam_test1.bam" ftype="bam"/>
38 <tests> 43 </test>
39 <test> 44 </tests>
40 <param name="inputFile" value="picard_AddCommentsToBam.bam" /> 45 <help>
41 <param name="comment" value="test1" />
42 <param name="validation_stringency" value="LENIENT" />
43 <output name="outFile" file="picard_AddCommentsToBam_test1.bam" ftype="bam" />
44 </test>
45 </tests>
46 <help>
47 46
48 .. class:: infomark 47 .. class:: infomark
49 48
50 **Purpose** 49 **Purpose**
51 50
58 COMMENT=String 57 COMMENT=String
59 C=String Comments to add to the BAM file This option may be specified 0 or more times. 58 C=String Comments to add to the BAM file This option may be specified 0 or more times.
60 59
61 @more_info@ 60 @more_info@
62 </help> 61 </help>
63 <expand macro="citations" /> 62 <expand macro="citations"/>
64 </tool> 63 </tool>