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comparison bam_dump.xml @ 27:8be4f23d1018

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Add bam-dump and test data.
author Matt Shirley <mdshw5@gmail.com>
date Mon, 30 Mar 2015 22:40:59 -0400
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children fdc981664a43
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26:7d80b2b24270 27:8be4f23d1018
1 <tool id="bam_dump" name="Extract reads" version="1.1.2">
2 <description> in BAM format from NCBI SRA.</description>
3 <command>
4 sam-dump --log-level fatal
5 #if str( $region ) != "":
6 --aligned-region $region
7 #end if
8 #if str( $matepairDist ) != "":
9 --matepair-distance $matepairDist
10 #end if
11 #if str( $minMapq ) != "":
12 --minmapq $minMapq
13 #end if
14 #if $header == "yes":
15 --header
16 #else:
17 --no-header
18 #end if
19 #if str( $alignments ) == "both":
20 --unaligned
21 #end if
22 #if str( $alignments ) == "unaligned":
23 --unaligned-spots-only
24 #end if
25 #if (str( $primary ) == "yes") and (str ( $alignments != "unaligned") ):
26 --primary
27 #end if
28 #if $input.input_select == "file":
29 $input.file
30 #elif $input.input_select == "accession_number":
31 $input.accession
32 #elif $input.input_select == "text":
33 `cat $input.text`
34 #end if
35 | samtools view -Sb - > $output
36 </command>
37 <version_string>sam-dump --version</version_string>
38 <inputs>
39 <conditional name="input">
40 <param name="input_select" type="select" label="select input type">
41 <option value="accession_number">SRR accession</option>
42 <option value="file">SRA archive in current history</option>
43 <option value="text">text file containing SRR accession</option>
44 </param>
45 <when value="file">
46 <param format="sra" name="file" type="data" label="sra archive"/>
47 </when>
48 <when value="accession_number">
49 <param format="text" name="accession" type="text" label="accession"/>
50 </when>
51 <when value="text">
52 <param format="txt" name="text" type="data" label="text file"/>
53 </when>
54 </conditional>
55 <param format="text" name="region" type="text" label="aligned region"/>
56 <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)"/>
57 <param format="text" name="header" type="select" value="yes">
58 <label>output BAM header</label>
59 <option value="yes">Yes</option>
60 <option value="no">No</option>
61 </param>
62 <param format="text" name="alignments" type="select" value="both">
63 <label>aligned or unaligned reads</label>
64 <option value="both">both</option>
65 <option value="aligned">aligned only</option>
66 <option value="unaligned">unaligned only</option>
67 </param>
68 <param format="text" name="primary" type="select" value="no">
69 <label>only primary aligments</label>
70 <option value="no">No</option>
71 <option value="yes">Yes</option>
72 </param>
73 <param format="text" name="minMapq" type="text" label="minimum mapping quality"/>
74 </inputs>
75 <outputs>
76 <data name="output" format="bam"/>
77 </outputs>
78 <requirements>
79 <requirement type="package" version="2.4.5">sra_toolkit</requirement>
80 <requirement type="package" version="1.2">samtools</requirement>
81 </requirements>
82 <help>
83 This tool extracts reads from sra archives using sam-dump.
84 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
85 The sam-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
86 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
87 </help>
88 </tool>