Mercurial > repos > devteam > picard
comparison picard_MergeSamFiles.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 | 2589e6207cb4 |
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2:93ace7e49295 | 3:52fdfc45590a |
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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 |