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comparison picard_MergeSamFiles.xml @ 0:b76a4f17bbbb draft

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author devteam
date Thu, 23 Oct 2014 11:31:30 -0400
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1 <tool name="MergeSamFiles" id="picard_MergeSamFiles" version="1.122.0">
2 <description>merges multiple SAM/BAM datasets into one</description>
3 <requirements>
4 <requirement type="package" version="1.122.0">picard</requirement>
5 </requirements>
6
7 <macros>
8 <import>picard_macros.xml</import>
9 </macros>
10
11 <command>
12 @java_options@
13
14 java -jar \$JAVA_JAR_PATH/MergeSamFiles.jar
15
16 #for $element in $inputFile:
17 INPUT="${element}"
18 #end for
19
20 OUTPUT="${outFile}"
21 MERGE_SEQUENCE_DICTIONARIES="${merge_sequence_dictionaries}"
22
23 ASSUME_SORTED="${assume_sorted}"
24 #for $element in $comments:
25 COMMENT="${element.comment}"
26 #end for
27
28 USE_THREADING=true
29 SORT_ORDER=coordinate
30 VALIDATION_STRINGENCY="${validation_stringency}"
31 QUIET=true
32 VERBOSITY=ERROR
33
34 </command>
35 <inputs>
36 <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
37 <param name="merge_sequence_dictionaries" type="boolean" label="Merge the sequence dictionaries of the datasets being merged" help="MERGE_SEQUENCE_DICTIONARIES; default=False"/>
38 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" help="ASSUME_SORTED; default=False"/>
39
40 <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments">
41 <param name="comment" type="text" size="50" label="Add this comment to BAM dataset" help="COMMENT"/>
42 </repeat>
43
44 <expand macro="VS" />
45
46 </inputs>
47
48 <outputs>
49 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Merged BAM dataset"/>
50 </outputs>
51
52 <tests>
53 <test>
54 <param name="inputFile" value="picard_MergeSamFiles_input1.bam,picard_MergeSamFiles_input2.bam,picard_MergeSamFiles_input3.bam" ftype="bam"/>
55 <param name="assume_sorted" value="False"/>
56 <param name="merge_sequence_dictionaries" value="False"/>
57 <param name="validation_stringency" value="LENIENT"/>
58 <output name="outFile" file="picard_MergeSamFiles_test1.bam" ftype="bam" lines_diff="2"/>
59 </test>
60 </tests>
61
62 <stdio>
63 <exit_code range="1:" level="fatal"/>
64 </stdio>
65
66 <help>
67
68 **Purpose**
69
70 Merges multiple SAM/BAM datasets into one.
71
72 @dataset_collections@
73
74 @description@
75
76 ASSUME_SORTED=Boolean
77 AS=Boolean If true, assume that the input files are in the same sort order as the requested output
78 sort order, even if their headers say otherwise. Default value: false. This option can
79 be set to 'null' to clear the default value. Possible values: {true, false}
80
81 MERGE_SEQUENCE_DICTIONARIES=Boolean
82 MSD=Boolean Merge the sequence dictionaries Default value: false. This option can be set to 'null'
83 to clear the default value. Possible values: {true, false}
84
85 COMMENT=String
86 CO=String Comment(s) to include in the merged output file's header. This option may be specified 0
87 or more times.
88
89
90 @more_info@
91
92 </help>
93 </tool>
94
95