Mercurial > repos > hepcat72 > lumpyexpress
comparison lumpyexpress.xml @ 0:e5150e64206a draft
planemo upload for repository https://github.com/hepcat72/robs_galaxy_tools/tree/master/tools/lumpyexpress commit 9c7264014db750b32a8fa78f511c7efbd12529d9-dirty
author | hepcat72 |
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date | Tue, 16 Oct 2018 15:55:49 -0400 |
parents | |
children | 107fa8e0b744 |
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1 <tool id="lumpyexpress_0_1" name="lumpyexpress" version="0.1.0"> | |
2 <description>Single or paired end SV detection</description> | |
3 | |
4 <requirements> | |
5 <requirement type="package" version="2.7">python</requirement> | |
6 <requirement type="package" version="0.8.3">pysam</requirement> | |
7 <requirement type="package" version="1.13.1">numpy</requirement> | |
8 <requirement type="package" version="0.2.14a">lumpy-sv</requirement> | |
9 <requirement type="package" version="1.9">samtools</requirement> | |
10 <requirement type="package" version="0.1.24">samblaster</requirement> | |
11 <requirement type="package" version="0.6.5">sambamba</requirement> | |
12 <requirement type="package" version="4.2.1">gawk</requirement> | |
13 </requirements> | |
14 | |
15 <version_command>___COMMAND___ ___VERSION_FLAG___</version_command> | |
16 | |
17 <command detect_errors="aggressive"> | |
18 <![CDATA[ | |
19 $__tool_directory__/lumpy_wrapper.tcsh | |
20 '$paired' | |
21 '$outfile' | |
22 #for $bam in $bams | |
23 '$bam' | |
24 #end for | |
25 ]]> | |
26 </command> | |
27 | |
28 <inputs> | |
29 <param format="bam" | |
30 name="bams" | |
31 label="Bam file(s)" | |
32 argument="argument positions 3-N" | |
33 | |
34 type="data" | |
35 multiple="true" | |
36 | |
37 help="Optionally sorted/indexed whole bam files. Splitters and discordants will be extracted from this file."/> | |
38 | |
39 <param name="paired" | |
40 label="Bam files contain paired end data" | |
41 argument="argument position 1" | |
42 | |
43 type="boolean" | |
44 truevalue="1" | |
45 falsevalue="0" | |
46 checked="no" | |
47 value="false"/> | |
48 </inputs> | |
49 | |
50 <outputs> | |
51 <data format="vcf" name="outfile" /> | |
52 </outputs> | |
53 | |
54 <tests> | |
55 <test> | |
56 <param name="bams" value="test1-1.bam,test1-2.bam,test1-3.bam"/> | |
57 <param name="paired" value="1"/> | |
58 <output name="outfile" file="lumpy-test1.vcf"/> | |
59 </test> | |
60 </tests> | |
61 | |
62 <help> | |
63 <![CDATA[ | |
64 Paired-end data is processed with lumpyexpress using only the required arguments. Single-end data is processed with lumpy using `-mw 4 -tt 0 -sr id:<SAMPLE>,bam_file:<SAMPLE>.splitters.bam,back_distance:10,weight:1,min_mapping_threshold:20`. Submit an issue to the tool wrapper repo if you would like more options to be available: https://github.com/hepcat72/robs_galaxy_tools | |
65 | |
66 Split reads and discordant reads are extracted from the supplied bam files. Each bam file should represent a different sample. | |
67 ]]> | |
68 </help> | |
69 | |
70 <citations> | |
71 <citation type="doi">10.1186/gb-2014-15-6-r84</citation> | |
72 </citations> | |
73 | |
74 </tool> |