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comparison sam_dump.xml @ 8:558a88cd49e4

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bump toolkit versions, old registration path
author Matt Shirley <mdshw5@gmail.com>
date Thu, 13 Mar 2014 16:11:04 -0400
parents 548b3e8d7a0a
children 393a04ec0fa9
comparison
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7:e724bff23fb6 8:558a88cd49e4
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
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
12 --minmapq $minMapq 12 --minmapq $minMapq
13 #end if 13 #end if
14 #if $header == "yes": 14 #if $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":
20 --unaligned 20 --unaligned
21 #end if 21 #end if
22 #if str( $alignments ) == "unaligned": 22 #if str( $alignments ) == "unaligned":
29 --fastq 29 --fastq
30 #end if 30 #end if
31 #if $input.input_select == "file": 31 #if $input.input_select == "file":
32 $input.file 32 $input.file
33 #elif $input.input_select == "accession_number": 33 #elif $input.input_select == "accession_number":
34 $input.accession 34 $input.accession
35 #elif $input.input_select == "text": 35 #elif $input.input_select == "text":
36 `cat $input.text` 36 `cat $input.text`
37 #end if 37 #end if
38 > $output 38 > $output
39 </command> 39 </command>
40 <version_string>sam-dump --version</version_string> 40 <version_string>sam-dump --version</version_string>
41 <inputs> 41 <inputs>
42 <conditional name="input"> 42 <conditional name="input">
43 <param name="input_select" type="select" label="select input type"> 43 <param name="input_select" type="select" label="select input type">
44 <option value="accession_number">SRR accession</option> 44 <option value="accession_number">SRR accession</option>
86 <when input="fastq" value="yes" format="fastq"/> 86 <when input="fastq" value="yes" format="fastq"/>
87 </change_format> 87 </change_format>
88 </data> 88 </data>
89 </outputs> 89 </outputs>
90 <requirements> 90 <requirements>
91 <requirement type="package" version="2.3.3-3">sra_toolkit</requirement> 91 <requirement type="package" version="2.3.4-2">sra_toolkit</requirement>
92 </requirements> 92 </requirements>
93 <help> 93 <help>
94 This tool extracts reads from sra archives using sam-dump. 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. 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. 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. 97 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
98 </help> 98 </help>
99 </tool> 99 </tool>