comparison sra_tools-04cc8176e86f/fastq_dump.xml @ 0:c386fe82db82

Initial commit, moving from test tool shed.
author matt-shirley
date Wed, 25 Sep 2013 21:00:05 -0400
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1 <tool id="fastq_dump" name="Extract reads" version="1.1.1">
2 <description> from NCBI SRA.</description>
3 <command>
4 fastq-dump --log-level fatal
5 #if $input.input_select == "file":
6 --accession '${input.file.name}'
7 #else:
8 --accession $input.accession
9 #end if
10 --defline-seq '@\$sn[_\$rn]/\$ri'
11 --stdout
12 #if $split == "yes":
13 --split-spot
14 #end if
15 #if str( $alignments ) == "aligned":
16 --aligned
17 #end if
18 #if str( $alignments ) == "unaligned":
19 --unaligned
20 #end if
21 #if str( $minID ) != "":
22 --minSpotId $minID
23 #end if
24 #if str( $maxID ) != "":
25 --maxSpotId $maxID
26 #end if
27 #if str( $minlen ) != "":
28 --minReadLen $minlen
29 #end if
30 #if str( $readfilter ) != "":
31 --read-filter $readfilter
32 #end if
33 #if str( $region ) != "":
34 --aligned-region $region
35 #end if
36 #if str( $spotgroups ) != "":
37 --spot-groups $spotgroups
38 #end if
39 #if str( $matepairDist ) != "":
40 --matepair-distance $matepairDist
41 #end if
42 #if $clip == "yes":
43 --clip
44 #end if
45 #if str( $outputformat ) == "fasta":
46 --fasta
47 #end if
48 #if $input.input_select=="file":
49 $input.file
50 #else:
51 $input.accession
52 #end if
53 > $output
54 </command>
55 <version_string>fastq-dump --version</version_string>
56 <inputs>
57 <conditional name="input">
58 <param name="input_select" type="select" label="select input type">
59 <option value="accession_number">SRR accession</option>
60 <option value="file">SRA archive in current history</option>
61 </param>
62 <when value="file">
63 <param format="sra" name="file" type="data" label="sra archive"/>
64 </when>
65 <when value="accession_number">
66 <param format="text" name="accession" type="text" label="accession"/>
67 </when>
68 </conditional>
69 <param format="text" name="minID" type="text" label="minimum spot ID"/>
70 <param format="text" name="maxID" type="text" label="maximum spot ID"/>
71 <param format="text" name="minlen" type="text" label="minimum read length"/>
72 <param format="text" name="split" type="select" value="yes">
73 <label>split spot by read pairs</label>
74 <option value="yes">Yes</option>
75 <option value="no">No</option>
76 </param>
77 <param format="text" name="alignments" type="select" value="both">
78 <label>aligned or unaligned reads</label>
79 <option value="both">both</option>
80 <option value="aligned">aligned only</option>
81 <option value="unaligned">unaligned only</option>
82 </param>
83 <param format="text" name="region" type="text" label="aligned region"/>
84 <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)"/>
85 <param format="text" name="readfilter" type="select" value="">
86 <label>filter by value</label>
87 <option value="">None</option>
88 <option value="pass">pass</option>
89 <option value="reject">reject</option>
90 <option value="criteria">criteria</option>
91 <option value="redacted">redacted</option>
92 </param>
93 <param name="outputformat" type="select" label="select output format">
94 <option value="fastqsanger">fastq</option>
95 <option value="fasta">fasta</option>
96 </param>
97 <param format="text" name="spotgroups" type="text" label="filter by spot-groups"/>
98 <param format="text" name="clip" type="select" value="no">
99 <label>apply left and right clips</label>
100 <option value="no">No</option>
101 <option value="yes">Yes</option>
102 </param>
103 </inputs>
104 <outputs>
105 <data format="fastq" name="output">
106 <change_format>
107 <when input="outputformat" value="fasta" format="fasta" />
108 </change_format>
109 </data>
110 </outputs>
111 <stdio>
112 <exit_code range="127" level="fatal" description="Could not locate fastq-dump binary"/>
113 </stdio>
114 <requirements>
115 <requirement type="package" version="2.3.3-3">sra_toolkit</requirement>
116 </requirements>
117 <help>
118 This tool extracts reads from SRA archives using fastq-dump.
119 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
120 The fastq-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
121 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
122 </help>
123 </tool>