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comparison picard_CleanSam.xml @ 8:e417b1d6288d 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 10:04:26 -0500
parents 08f69add4d06
children 41b8d087a2d2
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7:08f69add4d06 8:e417b1d6288d
4 <import>picard_macros.xml</import> 4 <import>picard_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 @java_options@ 8 @java_options@
9 @symlink_element_identifier@
9 picard 10 picard
10 CleanSam 11 CleanSam
11 INPUT="${inputFile}" 12 INPUT='$inputFile.element_identifier'
12 OUTPUT="${outFile}" 13 OUTPUT="${outFile}"
13 QUIET=true 14 QUIET=true
14 VERBOSITY=ERROR 15 VERBOSITY=ERROR
15 VALIDATION_STRINGENCY=${validation_stringency} 16 VALIDATION_STRINGENCY=${validation_stringency}
16 ]]></command> 17 ]]></command>
17 18
18 <inputs> 19 <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"/> 20 <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 21
21 <expand macro="VS" /> 22 <expand macro="VS" />
22 23
23 </inputs> 24 </inputs>
24 25
25 <outputs> 26 <outputs>
26 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: cleaned BAM dataset"> 27 <data name="outFile" format="bam" label="${tool.name} on ${on_string}: cleaned BAM dataset">
27 </data> 28 </data>
28 </outputs> 29 </outputs>
29 30
30 31
31 <tests> 32 <tests>
32 <test> 33 <test>
33 <param name="inputFile" ftype="bam" value="picard_CleanSam.bam" /> 34 <param name="inputFile" ftype="bam" value="picard_CleanSam.bam" />
34 <output name="outFile" file="picard_CleanSam_test1.bam" ftype="bam" /> 35 <output name="outFile" file="picard_CleanSam_test1.bam" ftype="bam" lines_diff="4"/>
35 </test> 36 </test>
36 </tests> 37 </tests>
37 38
38 <help> 39 <help>
39 40
40 .. class:: infomark 41 .. class:: infomark
41 42
42 **Purpose** 43 **Purpose**
43 44
44 Read SAM/BAM and perform various fix-ups. Currently, the only fix-ups are: 45 Read SAM/BAM and perform various fix-ups. Currently, the only fix-ups are:
45 46
46 1. to soft-clip an alignment that hangs off the end of its reference sequence. 47 1. to soft-clip an alignment that hangs off the end of its reference sequence.
47 2. to set MAPQ to 0 if a read is unmapped. 48 2. to set MAPQ to 0 if a read is unmapped.
48 49
49 @dataset_collections@ 50 @dataset_collections@
50 51
51 @more_info@ 52 @more_info@
52 53
53 </help> 54 </help>
54 </tool> 55 </tool>