Mercurial > repos > matt-shirley > ncbi_sra_toolkit

annotate sra_pileup.xml @ 24:22d9fe442c50

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
This is coming together.
author Matt Shirley <mdshw5@gmail.com>
date Mon, 30 Mar 2015 21:33:57 -0400
parents 293927a46697
children 393a04ec0fa9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
1 <tool id="sra_pileup" name="Generate pileup format" version="1.1.1">
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
2 <description> from NCBI sra.</description>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
3 <command>sra-pileup --log-level fatal
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
4 #if str( $region ) != "":
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
5 --aligned-region $region
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
6 #end if
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
7 #if str( $minMapq ) != "":
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
8 --minmapq $minMapq
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
9 #end if
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
10 #if $input.input_select == "file":
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
11 $input.file
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
12 #elif $input.input_select == "accession_number":
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
13 $input.accession
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
14 #elif $input.input_select == "text":
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
15 `cat $input.text`
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
16 #end if
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
17 > $output</command>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
18 <version_string>sra-pileup --version</version_string>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
19 <inputs>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
20 <conditional name="input">
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
21 <param name="input_select" type="select" label="select input type">
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
22 <option value="accession_number">SRR accession</option>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
23 <option value="file">SRA archive in current history</option>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
24 <option value="text">text file containing SRR accession</option>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
25 </param>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
26 <when value="file">
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
27 <param format="sra" name="file" type="data" label="sra archive"/>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
28 </when>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
29 <when value="accession_number">
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
30 <param format="text" name="accession" type="text" label="accession"/>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
31 </when>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
32 <when value="text">
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
33 <param format="txt" name="text" type="data" label="text file"/>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
34 </when>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
35 </conditional>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
36 <param format="text" name="region" type="text" label="aligned region"/>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
37 <param format="text" name="minMapq" type="text" label="minimum mapping quality"/>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
38 </inputs>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
39 <outputs>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
40 <data format="pileup" name="output"/>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
41 </outputs>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
42 <requirements>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
43 <requirement type="package" version="2.3.3-3">sra_toolkit</requirement>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
44 </requirements>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
45 <help>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
46 This tool produces pileup format from sra archives using sra-pileup.
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
47 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
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.
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
49 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
50 </help>
293927a46697 Move from test tool shed
Matt Shirley <mdshw5@gmail.com>
parents:
diff changeset
51 </tool>