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comparison sam_dump.xml @ 28:fdc981664a43

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Update to most recent GitHub version passing tests.
author Matt Shirley <mdshw5@gmail.com>
date Wed, 01 Apr 2015 12:35:38 -0400
parents 393a04ec0fa9
children
comparison
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27:8be4f23d1018 28:fdc981664a43
1 <tool id="sam_dump" name="Extract reads" version="1.1.2"> 1 <tool id="sam_dump" name="Extract reads" version="1.1.2">
2 <description> in SAM format from NCBI SRA.</description> 2 <description> in SAM format from NCBI SRA.</description>
3 <command> 3 <command>
4 sam-dump --log-level fatal 4 sam-dump --log-level fatal --disable-multithreading
5 #if str( $region ) != "": 5 #if str( $region ) != "":
6 --aligned-region $region 6 --aligned-region $region
7 #end if 7 #end if
8 #if str( $matepairDist ) != "": 8 #if str( $matepairDist ) != "":
9 --matepair-distance $matepairDist 9 --matepair-distance $matepairDist
10 #end if 10 #end if
11 #if str( $minMapq ) != "": 11 #if str( $minMapq ) != "":
12 --minmapq $minMapq 12 --minmapq $minMapq
13 #end if 13 #end if
14 #if $header == "yes": 14 #if str( $header ) == "yes":
15 --header 15 --header
16 #else: 16 #else:
17 --no-header 17 --no-header
18 #end if 18 #end if
19 #if str( $alignments ) == "both": 19 #if str( $alignments ) == "both":
23 --unaligned-spots-only 23 --unaligned-spots-only
24 #end if 24 #end if
25 #if (str( $primary ) == "yes") and (str ( $alignments != "unaligned") ): 25 #if (str( $primary ) == "yes") and (str ( $alignments != "unaligned") ):
26 --primary 26 --primary
27 #end if 27 #end if
28 #if str( $fastq ) == "yes":
29 --fastq
30 #end if
31 #if $input.input_select == "file": 28 #if $input.input_select == "file":
32 $input.file 29 $input.file
33 #elif $input.input_select == "accession_number": 30 #elif $input.input_select == "accession_number":
34 $input.accession 31 $input.accession
35 #elif $input.input_select == "text":
36 `cat $input.text`
37 #end if 32 #end if
38 > $output 33 > $output
39 </command> 34 </command>
40 <version_string>sam-dump --version</version_string> 35 <version_string>sam-dump --version</version_string>
41 <inputs> 36 <inputs>
42 <conditional name="input"> 37 <conditional name="input">
43 <param name="input_select" type="select" label="select input type"> 38 <param name="input_select" type="select" label="select input type">
44 <option value="accession_number">SRR accession</option> 39 <option value="accession_number">SRR accession</option>
45 <option value="file">SRA archive in current history</option> 40 <option value="file">SRA archive in current history</option>
46 <option value="text">text file containing SRR accession</option>
47 </param> 41 </param>
48 <when value="file"> 42 <when value="file">
49 <param format="sra" name="file" type="data" label="sra archive"/> 43 <param format="sra" name="file" type="data" label="sra archive"/>
50 </when> 44 </when>
51 <when value="accession_number"> 45 <when value="accession_number">
52 <param format="text" name="accession" type="text" label="accession"/> 46 <param format="text" name="accession" type="text" label="accession"/>
53 </when> 47 </when>
54 <when value="text">
55 <param format="txt" name="text" type="data" label="text file"/>
56 </when>
57 </conditional> 48 </conditional>
58 <param format="text" name="region" type="text" label="aligned region"/> 49 <param format="text" name="region" type="text" label="aligned region (chr:start-end)"/>
59 <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)"/> 50 <param format="text" name="matepairDist" type="text" label="mate-pair distance (from-to)"/>
60 <param format="text" name="header" type="select" value="yes"> 51 <param format="text" name="header" type="select" value="yes">
61 <label>output SAM header</label> 52 <label>output SAM header</label>
62 <option value="yes">Yes</option> 53 <option value="yes">Yes</option>
63 <option value="no">No</option> 54 <option value="no">No</option>
64 </param> 55 </param>
72 <label>only primary aligments</label> 63 <label>only primary aligments</label>
73 <option value="no">No</option> 64 <option value="no">No</option>
74 <option value="yes">Yes</option> 65 <option value="yes">Yes</option>
75 </param> 66 </param>
76 <param format="text" name="minMapq" type="text" label="minimum mapping quality"/> 67 <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> 68 </inputs>
83 <outputs> 69 <outputs>
84 <data name="output" format="sam"> 70 <data name="output" format="sam"/>
85 <change_format>
86 <when input="fastq" value="yes" format="fastq"/>
87 </change_format>
88 </data>
89 </outputs> 71 </outputs>
90 <requirements> 72 <requirements>
91 <requirement type="package" version="2.4.5">sra_toolkit</requirement> 73 <requirement type="package" version="2.4.5">sra_toolkit</requirement>
92 </requirements> 74 </requirements>
75 <tests>
76 <test>
77 <param name="input_select" value="accession_number"/>
78 <param name="accession" value="SRR925743"/>
79 <param name="region" value="17:41243452-41277500"/>
80 <output name="output" file="sam_dump_result.sam" ftype="sam" />
81 </test>
82 </tests>
93 <help> 83 <help>
94 This tool extracts reads from sra archives using sam-dump. 84 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. 85 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. 86 The sam-dump program is developed at NCBI, and is available at: http://github.com/ncbi/sra-tools
97 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. 87 Please submit inquiries and bug reports to http://github.com/mdshw5/sra-tools-galaxy.
98 </help> 88 </help>
99 </tool> 89 </tool>