Mercurial > repos > matt-shirley > sra_tools
comparison sra_pileup.xml @ 38:a0925f507352 draft
bring pileup to parity with sam; fixed minMapq for sam
author | Matt Shirley <mdshw5@gmail.com> |
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date | Sun, 04 Aug 2013 23:17:53 -0400 |
parents | 4985f8c00366 |
children | 3cb113532930 |
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37:4da2d7f0128e | 38:a0925f507352 |
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1 <tool id="sra_pileup" name="Generate pileup format" version="1.0.0"> | 1 <tool id="sra_pileup" name="Generate pileup format" version="1.0.1"> |
2 <description> from NCBI sra.</description> | 2 <description> from NCBI sra.</description> |
3 <command>sra-pileup '$input' > $output</command> | 3 <command>sra-pileup --log-level fatal |
4 #if str( $region ) != "": | |
5 --aligned-region $region | |
6 #end if | |
7 #if str( $minMapq ) != "": | |
8 --minmapq $minMapq | |
9 #end if | |
10 #if $input.input_select == "file": | |
11 $input.file | |
12 #else: | |
13 $input.accession | |
14 #end if | |
15 > $output</command> | |
4 <version_string>sra-pileup --version</version_string> | 16 <version_string>sra-pileup --version</version_string> |
5 <inputs> | 17 <inputs> |
6 <param format="sra" name="input" type="data" label="sra archive"/> | 18 <conditional name="input"> |
19 <param name="input_select" type="select" label="select input type"> | |
20 <option value="accession_number">SRR accession</option> | |
21 <option value="file">SRA archive in current history</option> | |
22 </param> | |
23 <when value="file"> | |
24 <param format="sra" name="file" type="data" label="sra archive"/> | |
25 </when> | |
26 <when value="accession_number"> | |
27 <param format="text" name="accession" type="text" label="accession"/> | |
28 </when> | |
29 </conditional> | |
30 <param format="text" name="region" type="text" label="aligned region"/> | |
31 <param format="text" name="minMapq" type="text" label="minimum mapping quality"/> | |
7 </inputs> | 32 </inputs> |
8 <outputs> | 33 <outputs> |
9 <data format="sam" name="output"/> | 34 <data format="pileup" name="output"/> |
10 </outputs> | 35 </outputs> |
11 <requirements> | 36 <requirements> |
12 <requirement type="package" version="2.3.2-4">sra_toolkit</requirement> | 37 <requirement type="package" version="2.3.2-4">sra_toolkit</requirement> |
13 </requirements> | 38 </requirements> |
14 <help> | 39 <help> |
15 !!! Note that this tool does not function correctly !!! | |
16 This tool produces pileup format from sra archives using sra-pileup. | 40 This tool produces pileup format from sra archives using sra-pileup. |
17 The sra-pileup program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. | 41 The sra-pileup program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. |
18 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. | 42 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. |
19 </help> | 43 </help> |
20 </tool> | 44 </tool> |