Mercurial > repos > devteam > picard

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
32:f9242e01365a 33:3f254c5ced1d
1 <tool name="FixMateInformation" id="picard_FixMateInformation" version="@TOOL_VERSION@.@WRAPPER_VERSION@"> 1 <tool name="FixMateInformation" id="picard_FixMateInformation" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
2 <description>ensure that all mate-pair information is in sync between each read and it's mate pair</description> 2 <description>ensure that all mate-pair information is in sync between each read and it's mate pair</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 picard 10 picard FixMateInformation
11 FixMateInformation 11 --INPUT '${inputFile}'
12 INPUT="${inputFile}" 12 --OUTPUT '${outFile}'
13 OUTPUT="${outFile}" 13 --ASSUME_SORTED ${assume_sorted}
14 ASSUME_SORTED=${assume_sorted} 14 --ADD_MATE_CIGAR ${add_mate_cigar}
15 ADD_MATE_CIGAR=${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 <expand macro="VS"/>
28 <expand macro="VS" /> 27 </inputs>
29 28 <outputs>
30 </inputs> 29 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM with fixed mates"/>
31 30 </outputs>
32 <outputs> 31 <tests>
33 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM with fixed mates"/> 32 <test>
34 </outputs> 33 <param name="inputFile" value="picard_FixMateInformation.bam" ftype="bam"/>
35 34 <param name="add_mate_cigar" value="True"/>
36 <tests> 35 <param name="assume_sorted" value="False"/>
37 <test> 36 <param name="validation_stringency" value="LENIENT"/>
38 <param name="inputFile" value="picard_FixMateInformation.bam" ftype="bam"/> 37 <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="4"/>
39 <param name="add_mate_cigar" value="True"/> 38 </test>
40 <param name="assume_sorted" value="False"/> 39 </tests>
41 <param name="validation_stringency" value="LENIENT"/> 40 <help>
42 <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="4"/>
43 </test>
44 </tests>
45
46
47 <help>
48 41
49 **Purpose** 42 **Purpose**
50 43
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. 44 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.
52 45
71 MC=Boolean Adds the mate CIGAR tag (MC) if true, does not if false. Default value: true. 64 MC=Boolean Adds the mate CIGAR tag (MC) if true, does not if false. Default value: true.
72 65
73 @more_info@ 66 @more_info@
74 67
75 </help> 68 </help>
76 <expand macro="citations" /> 69 <expand macro="citations"/>
77 </tool> 70 </tool>