annotate picard_MergeSamFiles.xml @ 1:f3e98264fbdd draft

Deleted selected files
author devteam
date Thu, 23 Oct 2014 11:34:04 -0400
parents b76a4f17bbbb
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
1 <tool name="MergeSamFiles" id="picard_MergeSamFiles" version="1.122.0">
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
2 <description>merges multiple SAM/BAM datasets into one</description>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
3 <requirements>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
4 <requirement type="package" version="1.122.0">picard</requirement>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
5 </requirements>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
6
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
7 <macros>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
8 <import>picard_macros.xml</import>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
9 </macros>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
10
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
11 <command>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
12 @java_options@
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
13
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
14 java -jar \$JAVA_JAR_PATH/MergeSamFiles.jar
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
15
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
16 #for $element in $inputFile:
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
17 INPUT="${element}"
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
18 #end for
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
19
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
20 OUTPUT="${outFile}"
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
21 MERGE_SEQUENCE_DICTIONARIES="${merge_sequence_dictionaries}"
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
22
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
23 ASSUME_SORTED="${assume_sorted}"
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
24 #for $element in $comments:
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
25 COMMENT="${element.comment}"
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
26 #end for
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
27
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
28 USE_THREADING=true
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
29 SORT_ORDER=coordinate
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
30 VALIDATION_STRINGENCY="${validation_stringency}"
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
31 QUIET=true
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
32 VERBOSITY=ERROR
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
33
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
34 </command>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
35 <inputs>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
36 <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
37 <param name="merge_sequence_dictionaries" type="boolean" label="Merge the sequence dictionaries of the datasets being merged" help="MERGE_SEQUENCE_DICTIONARIES; default=False"/>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
38 <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" help="ASSUME_SORTED; default=False"/>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
39
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
40 <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments">
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
41 <param name="comment" type="text" size="50" label="Add this comment to BAM dataset" help="COMMENT"/>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
42 </repeat>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
43
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
44 <expand macro="VS" />
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
45
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
46 </inputs>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
47
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
48 <outputs>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
49 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Merged BAM dataset"/>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
50 </outputs>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
51
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
52 <tests>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
53 <test>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
54 <param name="inputFile" value="picard_MergeSamFiles_input1.bam,picard_MergeSamFiles_input2.bam,picard_MergeSamFiles_input3.bam" ftype="bam"/>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
55 <param name="assume_sorted" value="False"/>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
56 <param name="merge_sequence_dictionaries" value="False"/>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
57 <param name="validation_stringency" value="LENIENT"/>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
58 <output name="outFile" file="picard_MergeSamFiles_test1.bam" ftype="bam" lines_diff="2"/>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
59 </test>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
60 </tests>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
61
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
62 <stdio>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
63 <exit_code range="1:" level="fatal"/>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
64 </stdio>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
65
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
66 <help>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
67
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
68 **Purpose**
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
69
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
70 Merges multiple SAM/BAM datasets into one.
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
71
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
72 @dataset_collections@
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
73
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
74 @description@
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
75
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
76 ASSUME_SORTED=Boolean
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
77 AS=Boolean If true, assume that the input files are in the same sort order as the requested output
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
78 sort order, even if their headers say otherwise. Default value: false. This option can
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
79 be set to 'null' to clear the default value. Possible values: {true, false}
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
80
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
81 MERGE_SEQUENCE_DICTIONARIES=Boolean
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
82 MSD=Boolean Merge the sequence dictionaries Default value: false. This option can be set to 'null'
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
83 to clear the default value. Possible values: {true, false}
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
84
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
85 COMMENT=String
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
86 CO=String Comment(s) to include in the merged output file's header. This option may be specified 0
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
87 or more times.
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
88
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
89
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
90 @more_info@
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
91
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
92 </help>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
93 </tool>
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
94
b76a4f17bbbb Uploaded
devteam
parents:
diff changeset
95