Mercurial > repos > matt-shirley > ncbi_sra_toolkit
annotate sam_dump.xml @ 20:281f34ece271
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author | Matt Shirley <mdshw5@gmail.com> |
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date | Mon, 30 Mar 2015 20:59:06 -0400 |
parents | 558a88cd49e4 |
children | 393a04ec0fa9 |
rev | line source |
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4 | 1 <tool id="sam_dump" name="Extract reads" version="1.1.2"> |
2 | 2 <description> in SAM format from NCBI SRA.</description> |
3 <command> | |
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4 sam-dump --log-level fatal |
2 | 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: | |
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parents:
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17 --no-header |
2 | 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": | |
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Matt Shirley <mdshw5@gmail.com>
parents:
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34 $input.accession |
2 | 35 #elif $input.input_select == "text": |
36 `cat $input.text` | |
37 #end if | |
38 > $output | |
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Matt Shirley <mdshw5@gmail.com>
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39 </command> |
2 | 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> | |
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91 <requirement type="package" version="2.3.4-2">sra_toolkit</requirement> |
2 | 92 </requirements> |
93 <help> | |
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parents:
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94 This tool extracts reads from sra archives using sam-dump. |
558a88cd49e4
bump toolkit versions, old registration path
Matt Shirley <mdshw5@gmail.com>
parents:
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diff
changeset
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95 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. |
2 | 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> | |
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558a88cd49e4
bump toolkit versions, old registration path
Matt Shirley <mdshw5@gmail.com>
parents:
4
diff
changeset
|
99 </tool> |