Mercurial > repos > devteam > picard
comparison picard_FixMateInformation.xml @ 3:52fdfc45590a draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author | devteam |
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date | Thu, 16 Jul 2015 15:32:31 -0400 |
parents | |
children | 08f69add4d06 |
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2:93ace7e49295 | 3:52fdfc45590a |
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1 <tool name="FixMateInformation" id="picard_FixMateInformation" version="@TOOL_VERSION@.0"> | |
2 <description>ensure that all mate-pair information is in sync between each read and it's mate pair</description> | |
3 <macros> | |
4 <import>picard_macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements" /> | |
7 <command> | |
8 @java_options@ | |
9 | |
10 java -jar \$JAVA_JAR_PATH/picard.jar | |
11 FixMateInformation | |
12 INPUT="${inputFile}" | |
13 OUTPUT="${outFile}" | |
14 ASSUME_SORTED=${assume_sorted} | |
15 ADD_MATE_CIGAR=${add_mate_cigar} | |
16 | |
17 SORT_ORDER=coordinate | |
18 VALIDATION_STRINGENCY="${validation_stringency}" | |
19 QUIET=true | |
20 VERBOSITY=ERROR | |
21 | |
22 </command> | |
23 <inputs> | |
24 <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> | |
25 <param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/> | |
26 <param name="assume_sorted" type="boolean" truevalue="True" falsevalue="False" label="Assume that the input file is QUERYNAME sorted" help="ASSUME_SORTED; default=False"/> | |
27 | |
28 <expand macro="VS" /> | |
29 | |
30 </inputs> | |
31 | |
32 <outputs> | |
33 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM with fixed mates"/> | |
34 </outputs> | |
35 | |
36 <tests> | |
37 <test> | |
38 <param name="inputFile" value="picard_FixMateInformation.bam" ftype="bam"/> | |
39 <param name="add_mate_cigar" value="True"/> | |
40 <param name="assume_sorted" value="False"/> | |
41 <param name="validation_stringency" value="LENIENT"/> | |
42 <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="2"/> | |
43 </test> | |
44 </tests> | |
45 | |
46 <stdio> | |
47 <exit_code range="1:" level="fatal"/> | |
48 </stdio> | |
49 | |
50 <help> | |
51 | |
52 **Purpose** | |
53 | |
54 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. | |
55 | |
56 ------ | |
57 | |
58 .. class:: warningmark | |
59 | |
60 **Warning on using ASSUME_SORTED option** | |
61 | |
62 Datasets imported into Galaxy are automatically coordinate sorted. So use this option (set it to True) only if you are sure that this is necessary. If you are not sure - a good rule of thumb | |
63 is to assume that the BAM you are working with is coordinate sorted. | |
64 | |
65 @dataset_collections@ | |
66 | |
67 @description@ | |
68 | |
69 ASSUME_SORTED=Boolean | |
70 AS=Boolean If true, assume that the input file is queryname sorted, even if the header says | |
71 otherwise. Default value: false. | |
72 | |
73 ADD_MATE_CIGAR=Boolean | |
74 MC=Boolean Adds the mate CIGAR tag (MC) if true, does not if false. Default value: true. | |
75 | |
76 @more_info@ | |
77 | |
78 </help> | |
79 </tool> | |
80 | |
81 |