Mercurial > repos > matt-shirley > ncbi_sra_toolkit

comparison bam_dump.xml @ 28:fdc981664a43

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Update to most recent GitHub version passing tests.
author Matt Shirley <mdshw5@gmail.com>
date Wed, 01 Apr 2015 12:35:38 -0400
parents 8be4f23d1018
children
comparison
equal deleted inserted replaced
27:8be4f23d1018 28:fdc981664a43
1 <tool id="bam_dump" name="Extract reads" version="1.1.2"> 1 <tool id="bam_dump" name="Extract reads" version="1.1.2">
2 <description> in BAM format from NCBI SRA.</description> 2 <description> in BAM 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":
27 #end if 27 #end if
28 #if $input.input_select == "file": 28 #if $input.input_select == "file":
29 $input.file 29 $input.file
30 #elif $input.input_select == "accession_number": 30 #elif $input.input_select == "accession_number":
31 $input.accession 31 $input.accession
32 #elif $input.input_select == "text":
33 `cat $input.text`
34 #end if 32 #end if
35 | samtools view -Sb - > $output 33 | samtools view -Sb - 2> /dev/null > $output
36 </command> 34 </command>
37 <version_string>sam-dump --version</version_string> 35 <version_string>sam-dump --version</version_string>
38 <inputs> 36 <inputs>
39 <conditional name="input"> 37 <conditional name="input">
40 <param name="input_select" type="select" label="select input type"> 38 <param name="input_select" type="select" label="select input type">
41 <option value="accession_number">SRR accession</option> 39 <option value="accession_number">SRR accession</option>
42 <option value="file">SRA archive in current history</option> 40 <option value="file">SRA archive in current history</option>
43 <option value="text">text file containing SRR accession</option>
44 </param> 41 </param>
45 <when value="file"> 42 <when value="file">
46 <param format="sra" name="file" type="data" label="sra archive"/> 43 <param format="sra" name="file" type="data" label="sra archive"/>
47 </when> 44 </when>
48 <when value="accession_number"> 45 <when value="accession_number">
49 <param format="text" name="accession" type="text" label="accession"/> 46 <param format="text" name="accession" type="text" label="accession"/>
50 </when> 47 </when>
51 <when value="text">
52 <param format="txt" name="text" type="data" label="text file"/>
53 </when>
54 </conditional> 48 </conditional>
55 <param format="text" name="region" type="text" label="aligned region"/> 49 <param format="text" name="region" type="text" label="aligned region (chr:start-end)"/>
56 <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)"/>
57 <param format="text" name="header" type="select" value="yes"> 51 <param format="text" name="header" type="select" value="yes">
58 <label>output BAM header</label> 52 <label>output BAM header</label>
59 <option value="yes">Yes</option> 53 <option value="yes">Yes</option>
60 <option value="no">No</option> 54 <option value="no">No</option>
61 </param> 55 </param>
73 <param format="text" name="minMapq" type="text" label="minimum mapping quality"/> 67 <param format="text" name="minMapq" type="text" label="minimum mapping quality"/>
74 </inputs> 68 </inputs>
75 <outputs> 69 <outputs>
76 <data name="output" format="bam"/> 70 <data name="output" format="bam"/>
77 </outputs> 71 </outputs>
72 <stdio>
73 <exit_code range="127" level="fatal" description="Could not locate sam-dump and/or samtools binary"/>
74 </stdio>
78 <requirements> 75 <requirements>
79 <requirement type="package" version="2.4.5">sra_toolkit</requirement> 76 <requirement type="package" version="2.4.5">sra_toolkit</requirement>
80 <requirement type="package" version="1.2">samtools</requirement> 77 <requirement type="package" version="1.2">samtools</requirement>
81 </requirements> 78 </requirements>
79 <tests>
80 <test>
81 <param name="input_select" value="accession_number"/>
82 <param name="accession" value="SRR925743"/>
83 <param name="region" value="17:41243452-41277500"/>
84 <output name="output" file="bam_dump_result.bam" ftype="bam" />
85 </test>
86 </tests>
82 <help> 87 <help>
83 This tool extracts reads from sra archives using sam-dump. 88 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. 89 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. 90 The sam-dump program is developed at NCBI, and is available at: http://github.com/ncbi/sra-tools
86 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. 91 Please submit inquiries and bug reports to http://github.com/mdshw5/sra-tools-galaxy.
87 </help> 92 </help>
88 </tool> 93 </tool>