Mercurial > repos > mvdbeek > test_sra

annotate sra_pileup.xml @ 0:ec8b334b5ebb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
author mvdbeek
date Fri, 14 Aug 2015 12:23:28 -0400
parents
children 2c5483e80fb7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
1 <tool id="sra_pileup" name="Generate pileup format" version="1.1.1">
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
2 <description> from NCBI sra.</description>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
3 <command>sra-pileup --log-level fatal
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
4 #if str( $region ) != "":
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
5 --aligned-region $region
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
6 #end if
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
7 #if str( $minMapq ) != "":
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
8 --minmapq $minMapq
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
9 #end if
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
10 #if $input.input_select == "file":
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
11 $input.file
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
12 #elif $input.input_select == "accession_number":
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
13 $input.accession
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
14 #elif $input.input_select == "text":
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
15 `cat $input.text`
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
16 #end if
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
17 > $output</command>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
18 <version_string>sra-pileup --version</version_string>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
19 <inputs>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
20 <conditional name="input">
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
21 <param name="input_select" type="select" label="select input type">
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
22 <option value="accession_number">SRR accession</option>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
23 <option value="file">SRA archive in current history</option>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
24 <option value="text">text file containing SRR accession</option>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
25 </param>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
26 <when value="file">
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
27 <param format="sra" name="file" type="data" label="sra archive"/>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
28 </when>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
29 <when value="accession_number">
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
30 <param format="text" name="accession" type="text" label="accession"/>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
31 </when>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
32 <when value="text">
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
33 <param format="txt" name="text" type="data" label="text file"/>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
34 </when>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
35 </conditional>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
36 <param format="text" name="region" type="text" label="aligned region"/>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
37 <param format="text" name="minMapq" type="text" label="minimum mapping quality"/>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
38 </inputs>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
39 <outputs>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
40 <data format="pileup" name="output"/>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
41 </outputs>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
42 <requirements>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
43 <requirement type="package" version="2.4.5">sra_toolkit</requirement>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
44 </requirements>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
45 <tests>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
46 <test>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
47 <param name="input_select" value="accession_number"/>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
48 <param name="accession" value="SRR925743"/>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
49 <param name="region" value="17:41243452-41277500"/>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
50 <output name="output" file="sra_pileup_result.pileup" ftype="pileup" />
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
51 </test>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
52 </tests>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
53 <help>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
54 This tool produces pileup format from sra archives using sra-pileup.
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
55 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
56 The sra-pileup program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software.
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
57 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
58 </help>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
59 </tool>