Mercurial > repos > devteam > bam_to_sam
comparison bam_to_sam.xml @ 0:c9e926d9d87e draft
Uploaded tool tarball with dependencies.
author | devteam |
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date | Tue, 20 Aug 2013 09:19:46 -0400 |
parents | |
children | 38859774da87 |
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-1:000000000000 | 0:c9e926d9d87e |
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1 <tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.3"> | |
2 <requirements> | |
3 <requirement type="package" version="0.1.18">samtools</requirement> | |
4 </requirements> | |
5 <description>converts BAM format to SAM format</description> | |
6 <command interpreter="python"> | |
7 bam_to_sam.py | |
8 --input1=$input1 | |
9 --output1=$output1 | |
10 $header | |
11 </command> | |
12 <inputs> | |
13 <param name="input1" type="data" format="bam" label="BAM File to Convert" /> | |
14 <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" label="Include header in output" /> | |
15 </inputs> | |
16 <outputs> | |
17 <data format="sam" name="output1" label="${tool.name} on ${on_string}: converted SAM" /> | |
18 </outputs> | |
19 <tests> | |
20 <test> | |
21 <!-- | |
22 Bam-to-Sam command: | |
23 samtools view -o bam_to_sam_out1.sam test-data/bam_to_sam_in1.bam | |
24 bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam | |
25 --> | |
26 <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" /> | |
27 <param name="header" value="" /> | |
28 <output name="output1" file="bam_to_sam_out1.sam" sorted="True" /> | |
29 </test> | |
30 <test> | |
31 <!-- | |
32 Bam-to-Sam command: | |
33 samtools view -o bam_to_sam_out2.sam test-data/bam_to_sam_in2.bam | |
34 bam_to_sam_in2.bam can be created from bam_to_sam_in2.sam | |
35 --> | |
36 <param name="input1" value="bam_to_sam_in2.bam" ftype="bam" /> | |
37 <param name="header" value="" /> | |
38 <output name="output1" file="bam_to_sam_out2.sam" sorted="True" /> | |
39 </test> | |
40 <test> | |
41 <!-- | |
42 Bam-to-Sam command: | |
43 samtools view -h -o bam_to_sam_out3.sam test-data/bam_to_sam_in1.bam | |
44 bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam | |
45 --> | |
46 <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" /> | |
47 <param name="header" value="--header" /> | |
48 <output name="output1" file="bam_to_sam_out3.sam" sorted="True" lines_diff="6" /><!-- header param not working in func tests so won't produce correct 6-line header (fine in browser) --> | |
49 </test> | |
50 </tests> | |
51 <help> | |
52 | |
53 **What it does** | |
54 | |
55 This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file. | |
56 | |
57 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml | |
58 | |
59 ------ | |
60 | |
61 **Citation** | |
62 | |
63 For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ | |
64 | |
65 </help> | |
66 </tool> |