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comparison picard_MergeSamFiles.xml @ 3:52fdfc45590a draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Thu, 16 Jul 2015 15:32:31 -0400
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children 2589e6207cb4
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2:93ace7e49295 3:52fdfc45590a
1 <tool name="MergeSamFiles" id="picard_MergeSamFiles" version="@TOOL_VERSION@.0">
2 <description>merges multiple SAM/BAM datasets into one</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 MergeSamFiles
12
13 #for $element in $inputFile:
14 INPUT="${element}"
15 #end for
16
17 OUTPUT="${outFile}"
18 MERGE_SEQUENCE_DICTIONARIES="${merge_sequence_dictionaries}"
19
20 ASSUME_SORTED="${assume_sorted}"
21 #for $element in $comments:
22 COMMENT="${element.comment}"
23 #end for
24
25 USE_THREADING=true
26 SORT_ORDER=coordinate
27 VALIDATION_STRINGENCY="${validation_stringency}"
28 QUIET=true
29 VERBOSITY=ERROR
30
31 </command>
32 <inputs>
33 <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
34 <param name="merge_sequence_dictionaries" type="boolean" label="Merge the sequence dictionaries of the datasets being merged" help="MERGE_SEQUENCE_DICTIONARIES; default=False"/>
35 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" help="ASSUME_SORTED; default=False"/>
36
37 <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments">
38 <param name="comment" type="text" size="50" label="Add this comment to BAM dataset" help="COMMENT"/>
39 </repeat>
40
41 <expand macro="VS" />
42
43 </inputs>
44
45 <outputs>
46 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Merged BAM dataset"/>
47 </outputs>
48
49 <tests>
50 <test>
51 <param name="inputFile" value="picard_MergeSamFiles_input1.bam,picard_MergeSamFiles_input2.bam,picard_MergeSamFiles_input3.bam" ftype="bam"/>
52 <param name="assume_sorted" value="False"/>
53 <param name="merge_sequence_dictionaries" value="False"/>
54 <param name="validation_stringency" value="LENIENT"/>
55 <output name="outFile" file="picard_MergeSamFiles_test1.bam" ftype="bam" lines_diff="2"/>
56 </test>
57 </tests>
58
59 <stdio>
60 <exit_code range="1:" level="fatal"/>
61 </stdio>
62
63 <help>
64
65 **Purpose**
66
67 Merges multiple SAM/BAM datasets into one.
68
69 @dataset_collections@
70
71 @description@
72
73 ASSUME_SORTED=Boolean
74 AS=Boolean If true, assume that the input files are in the same sort order as the requested output
75 sort order, even if their headers say otherwise. Default value: false. This option can
76 be set to 'null' to clear the default value. Possible values: {true, false}
77
78 MERGE_SEQUENCE_DICTIONARIES=Boolean
79 MSD=Boolean Merge the sequence dictionaries Default value: false. This option can be set to 'null'
80 to clear the default value. Possible values: {true, false}
81
82 COMMENT=String
83 CO=String Comment(s) to include in the merged output file's header. This option may be specified 0
84 or more times.
85
86
87 @more_info@
88
89 </help>
90 </tool>
91
92