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comparison picard_FixMateInformation.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 486d7500da69
comparison
equal deleted inserted replaced
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
10 picard 9 picard
11 FixMateInformation 10 FixMateInformation
12 INPUT="${inputFile}" 11 INPUT="${inputFile}"
13 OUTPUT="${outFile}" 12 OUTPUT="${outFile}"
14 ASSUME_SORTED=${assume_sorted} 13 ASSUME_SORTED=${assume_sorted}
15 ADD_MATE_CIGAR=${add_mate_cigar} 14 ADD_MATE_CIGAR=${add_mate_cigar}
16 15
17 SORT_ORDER=coordinate 16 SORT_ORDER=coordinate
18 VALIDATION_STRINGENCY="${validation_stringency}" 17 VALIDATION_STRINGENCY="${validation_stringency}"
19 QUIET=true 18 QUIET=true
20 VERBOSITY=ERROR 19 VERBOSITY=ERROR
21 20
22 ]]></command> 21 ]]></command>
23 <inputs> 22 <inputs>
24 <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> 23 <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
25 <param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/> 24 <param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/>
26 <param name="assume_sorted" type="boolean" truevalue="True" falsevalue="False" label="Assume that the input file is QUERYNAME sorted" help="ASSUME_SORTED; default=False"/> 25 <param name="assume_sorted" type="boolean" truevalue="True" falsevalue="False" label="Assume that the input file is QUERYNAME sorted" help="ASSUME_SORTED; default=False"/>
27 26
28 <expand macro="VS" /> 27 <expand macro="VS" />
29 28
30 </inputs> 29 </inputs>
31 30
32 <outputs> 31 <outputs>
33 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM with fixed mates"/> 32 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM with fixed mates"/>
34 </outputs> 33 </outputs>
35 34
36 <tests> 35 <tests>
37 <test> 36 <test>
38 <param name="inputFile" value="picard_FixMateInformation.bam" ftype="bam"/> 37 <param name="inputFile" value="picard_FixMateInformation.bam" ftype="bam"/>
39 <param name="add_mate_cigar" value="True"/> 38 <param name="add_mate_cigar" value="True"/>
40 <param name="assume_sorted" value="False"/> 39 <param name="assume_sorted" value="False"/>
41 <param name="validation_stringency" value="LENIENT"/> 40 <param name="validation_stringency" value="LENIENT"/>
42 <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="4"/> 41 <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="4"/>
43 </test> 42 </test>
44 </tests> 43 </tests>
45 44
46 45
47 <help> 46 <help>
48 47
49 **Purpose** 48 **Purpose**
50 49
51 Ensure that all mate-pair information is in sync between each read and it's mate pair. Reads marked with the secondary alignment flag are written to the output file unchanged. 50 Ensure that all mate-pair information is in sync between each read and it's mate pair. Reads marked with the secondary alignment flag are written to the output file unchanged.
62 @dataset_collections@ 61 @dataset_collections@
63 62
64 @description@ 63 @description@
65 64
66 ASSUME_SORTED=Boolean 65 ASSUME_SORTED=Boolean
67 AS=Boolean If true, assume that the input file is queryname sorted, even if the header says 66 AS=Boolean If true, assume that the input file is queryname sorted, even if the header says
68 otherwise. Default value: false. 67 otherwise. Default value: false.
69 68
70 ADD_MATE_CIGAR=Boolean 69 ADD_MATE_CIGAR=Boolean
71 MC=Boolean Adds the mate CIGAR tag (MC) if true, does not if false. Default value: true. 70 MC=Boolean Adds the mate CIGAR tag (MC) if true, does not if false. Default value: true.
72 71
73 @more_info@ 72 @more_info@
74 73
75 </help> 74 </help>
76 </tool> 75 </tool>
77 76