Mercurial > repos > matt-shirley > ncbi_sra_toolkit

comparison sra_pileup.xml @ 25:393a04ec0fa9

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Update tool requirement versions.
author Matt Shirley <mdshw5@gmail.com>
date Mon, 30 Mar 2015 21:57:40 -0400
parents 293927a46697
children fdc981664a43
comparison
equal deleted inserted replaced
24:22d9fe442c50 25:393a04ec0fa9
1 <tool id="sra_pileup" name="Generate pileup format" version="1.1.1"> 1 <tool id="sra_pileup" name="Generate pileup format" version="1.1.1">
2 <description> from NCBI sra.</description> 2 <description> from NCBI sra.</description>
3 <command>sra-pileup --log-level fatal 3 <command>sra-pileup --log-level fatal
4 #if str( $region ) != "": 4 #if str( $region ) != "":
5 --aligned-region $region 5 --aligned-region $region
6 #end if 6 #end if
7 #if str( $minMapq ) != "": 7 #if str( $minMapq ) != "":
8 --minmapq $minMapq 8 --minmapq $minMapq
9 #end if 9 #end if
10 #if $input.input_select == "file": 10 #if $input.input_select == "file":
11 $input.file 11 $input.file
12 #elif $input.input_select == "accession_number": 12 #elif $input.input_select == "accession_number":
13 $input.accession 13 $input.accession
14 #elif $input.input_select == "text": 14 #elif $input.input_select == "text":
15 `cat $input.text` 15 `cat $input.text`
16 #end if 16 #end if
17 > $output</command> 17 > $output</command>
18 <version_string>sra-pileup --version</version_string> 18 <version_string>sra-pileup --version</version_string>
38 </inputs> 38 </inputs>
39 <outputs> 39 <outputs>
40 <data format="pileup" name="output"/> 40 <data format="pileup" name="output"/>
41 </outputs> 41 </outputs>
42 <requirements> 42 <requirements>
43 <requirement type="package" version="2.3.3-3">sra_toolkit</requirement> 43 <requirement type="package" version="2.4.5">sra_toolkit</requirement>
44 </requirements> 44 </requirements>
45 <help> 45 <help>
46 This tool produces pileup format from sra archives using sra-pileup. 46 This tool produces pileup format from sra archives using sra-pileup.
47 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. 47 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
48 The sra-pileup program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. 48 The sra-pileup program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
49 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. 49 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
50 </help> 50 </help>
51 </tool> 51 </tool>