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comparison picard_CleanSam.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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32:f9242e01365a 33:3f254c5ced1d
1 <tool id="picard_CleanSam" name="CleanSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool id="picard_CleanSam" name="CleanSam" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
2 <description>perform SAM/BAM grooming</description> 2 <description>perform SAM/BAM grooming</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 @symlink_element_identifier@
11 picard 11 picard CleanSam
12 CleanSam 12 --INPUT '$escaped_element_identifier'
13 INPUT='$escaped_element_identifier' 13 --OUTPUT '${outFile}'
14 OUTPUT="${outFile}" 14 --QUIET true
15 QUIET=true 15 --VERBOSITY ERROR
16 VERBOSITY=ERROR 16 --VALIDATION_STRINGENCY ${validation_stringency}
17 VALIDATION_STRINGENCY=${validation_stringency}
18 ]]></command> 17 ]]></command>
19 18 <inputs>
20 <inputs> 19 <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"/>
21 <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"/> 20 <expand macro="VS"/>
22 21 </inputs>
23 <expand macro="VS" /> 22 <outputs>
24 23 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: cleaned BAM dataset">
25 </inputs>
26
27 <outputs>
28 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: cleaned BAM dataset">
29 </data> 24 </data>
30 </outputs> 25 </outputs>
31 26 <tests>
32 27 <test>
33 <tests> 28 <param name="inputFile" ftype="bam" value="picard_CleanSam.bam"/>
34 <test> 29 <output name="outFile" file="picard_CleanSam_test1.bam" ftype="bam" lines_diff="4"/>
35 <param name="inputFile" ftype="bam" value="picard_CleanSam.bam" /> 30 </test>
36 <output name="outFile" file="picard_CleanSam_test1.bam" ftype="bam" lines_diff="4"/> 31 </tests>
37 </test> 32 <help>
38 </tests>
39
40 <help>
41 33
42 .. class:: infomark 34 .. class:: infomark
43 35
44 **Purpose** 36 **Purpose**
45 37
51 @dataset_collections@ 43 @dataset_collections@
52 44
53 @more_info@ 45 @more_info@
54 46
55 </help> 47 </help>
56 <expand macro="citations" /> 48 <expand macro="citations"/>
57 </tool> 49 </tool>