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comparison picard_MergeSam.xml @ 68:783087253ef4 draft

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author devteam
date Wed, 19 Feb 2014 17:57:55 -0500
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67:fda8c1757585 68:783087253ef4
1 <tool id="picard_mergesam" name="Merge SAM or BAM files" version="1.106.0">
2 <!-- Documentation: http://picard.sourceforge.net/command-line-overview.shtml#MergeSamFiles
3 Merges multiple SAM/BAM files into one file.
4 -->
5 <description>merges SAM or BAM files together</description>
6 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
7 <command interpreter="bash">
8 mergesam_wrapper.sh $output1 $outformat I=$input1 I=$input2
9 #for $i in $inputs
10 I=${i.input}
11 #end for
12 MSD=$mergeSD VALIDATION_STRINGENCY=LENIENT TMP_DIR=$__new_file_path__
13 2&gt; $outlog
14 ##|| echo "Error running Picard MergeSamFiles" >&amp;2
15 </command>
16 <inputs>
17 <param name="title" label="Name for the output merged bam file" type="text" default="Merged.bam"
18 help="This name will appear in your history so use it to remember what the new file in your history contains" />
19 <param name="outformat" type="select" label="Output format" >
20 <option value="bam" selected="True">BAM</option>
21 <option value="sam">SAM</option>
22 </param>
23 <param name="mergeSD" value="true" type="boolean" label="Merge all component bam file headers into the merged bam file"
24 truevalue="true" falsevalue="false" checked="yes"
25 help="Control the MERGE_SEQUENCE_DICTIONARIES flag for Picard MergeSamFiles. Default (true) correctly propagates read groups and other important metadata" />
26 <param name="input1" label="First file" type="data" format="bam,sam" />
27 <param name="input2" label="with file" type="data" format="bam,sam" help="Need to add more files? Use controls below." />
28 <repeat name="inputs" title="Input Files">
29 <param name="input" label="Add file" type="data" format="bam,sam" />
30 </repeat>
31 </inputs>
32 <outputs>
33 <data format="bam" name="output1" label="${title}.${outformat}" >
34 <change_format>
35 <when input="outformat" value="sam" format="sam" />
36 </change_format>
37 </data>
38 <data format="txt" name="outlog" label="${title}_${tool.name}.log" />
39 </outputs>
40 <tests>
41 <!-- TODO: add ability to test framework to test without at least
42 one repeat element value
43 -->
44 <test>
45 <param name="title" value="test1" />
46 <param name="mergeSD" value="true" />
47 <param name="input1" value="sam_merge_in1.bam" ftype="bam" />
48 <param name="input2" value="sam_merge_in2.bam" ftype="bam" />
49 <output name="output1" file="sam_merge_out1.bam" ftype="bam" />
50 <output name="outlog" file="sam_merge_out1.log" ftype="txt" lines_diff="11"/>
51 </test>
52 <test>
53 <param name="title" value="test2" />
54 <param name="mergeSD" value="true" />
55 <param name="input1" value="sam_merge_in1.bam" ftype="bam" />
56 <param name="input2" value="sam_merge_in2.bam" ftype="bam" />
57 <param name="input" value="sam_merge_in3.bam" ftype="bam" />
58 <output name="output1" file="sam_merge_out2.bam" ftype="bam" />
59 <output name="outlog" file="sam_merge_out2.log" ftype="txt" lines_diff="11"/>
60 </test>
61 </tests>
62 <help>
63
64 **What it does**
65
66 This tool uses the Picard_ merge command to merge any number of BAM files together into one BAM file while preserving the BAM
67 metadata such as read groups
68
69 .. _Picard: http://picard.sourceforge.net/command-line-overview.shtml#MergeSamFiles
70
71 </help>
72 </tool>