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comparison sam_dump.xml @ 2:293927a46697

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Move from test tool shed
author Matt Shirley <mdshw5@gmail.com>
date Wed, 25 Sep 2013 21:08:40 -0400
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1:da2dbe22f80b 2:293927a46697
1 <tool id="sam_dump" name="Extract reads" version="1.1.1">
2 <description> in SAM 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 str( $fastq ) == "yes":
29 --fastq
30 #end if
31 #if $input.input_select == "file":
32 $input.file
33 #elif $input.input_select == "accession_number":
34 $input.accession
35 #elif $input.input_select == "text":
36 `cat $input.text`
37 #end if
38 > $output
39 </command>
40 <version_string>sam-dump --version</version_string>
41 <inputs>
42 <conditional name="input">
43 <param name="input_select" type="select" label="select input type">
44 <option value="accession_number">SRR accession</option>
45 <option value="file">SRA archive in current history</option>
46 <option value="text">text file containing SRR accession</option>
47 </param>
48 <when value="file">
49 <param format="sra" name="file" type="data" label="sra archive"/>
50 </when>
51 <when value="accession_number">
52 <param format="text" name="accession" type="text" label="accession"/>
53 </when>
54 <when value="text">
55 <param format="txt" name="text" type="data" label="text file"/>
56 </when>
57 </conditional>
58 <param format="text" name="region" type="text" label="aligned region"/>
59 <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)"/>
60 <param format="text" name="header" type="select" value="yes">
61 <label>output SAM header</label>
62 <option value="yes">Yes</option>
63 <option value="no">No</option>
64 </param>
65 <param format="text" name="alignments" type="select" value="both">
66 <label>aligned or unaligned reads</label>
67 <option value="both">both</option>
68 <option value="aligned">aligned only</option>
69 <option value="unaligned">unaligned only</option>
70 </param>
71 <param format="text" name="primary" type="select" value="no">
72 <label>only primary aligments</label>
73 <option value="no">No</option>
74 <option value="yes">Yes</option>
75 </param>
76 <param format="text" name="minMapq" type="text" label="minimum mapping quality"/>
77 <param format="text" name="fastq" type="select" value="no">
78 <label>output fastq</label>
79 <option value="no">No</option>
80 <option value="yes">Yes</option>
81 </param>
82 </inputs>
83 <outputs>
84 <data name="output" format="sam">
85 <change_format>
86 <when input="fastq" value="yes" format="fastq"/>
87 </change_format>
88 </data>
89 </outputs>
90 <requirements>
91 <requirement type="package" version="2.3.3-3">sra_toolkit</requirement>
92 </requirements>
93 <help>
94 This tool extracts reads from sra archives using sam-dump.
95 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
96 The sam-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
97 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
98 </help>
99 </tool>