Mercurial > repos > matt-shirley > sra_tools
view 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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<tool id="sra_pileup" name="Generate pileup format" version="1.0.1"> <description> from NCBI sra.</description> <command>sra-pileup --log-level fatal #if str( $region ) != "": --aligned-region $region #end if #if str( $minMapq ) != "": --minmapq $minMapq #end if #if $input.input_select == "file": $input.file #else: $input.accession #end if > $output</command> <version_string>sra-pileup --version</version_string> <inputs> <conditional name="input"> <param name="input_select" type="select" label="select input type"> <option value="accession_number">SRR accession</option> <option value="file">SRA archive in current history</option> </param> <when value="file"> <param format="sra" name="file" type="data" label="sra archive"/> </when> <when value="accession_number"> <param format="text" name="accession" type="text" label="accession"/> </when> </conditional> <param format="text" name="region" type="text" label="aligned region"/> <param format="text" name="minMapq" type="text" label="minimum mapping quality"/> </inputs> <outputs> <data format="pileup" name="output"/> </outputs> <requirements> <requirement type="package" version="2.3.2-4">sra_toolkit</requirement> </requirements> <help> This tool produces pileup format from sra archives using sra-pileup. The sra-pileup program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. </help> </tool>