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annotate sra_pileup.xml @ 38:a0925f507352 draft

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bring pileup to parity with sam; fixed minMapq for sam
author Matt Shirley <mdshw5@gmail.com>
date Sun, 04 Aug 2013 23:17:53 -0400
parents 4985f8c00366
children 3cb113532930
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a0925f507352 bring pileup to parity with sam; fixed minMapq for sam
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1 <tool id="sra_pileup" name="Generate pileup format" version="1.0.1">
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2 <description> from NCBI sra.</description>
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3 <command>sra-pileup --log-level fatal
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4 #if str( $region ) != "":
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5 --aligned-region $region
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6 #end if
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7 #if str( $minMapq ) != "":
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8 --minmapq $minMapq
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9 #end if
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10 #if $input.input_select == "file":
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11 $input.file
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12 #else:
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13 $input.accession
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14 #end if
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15 > $output</command>
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16 <version_string>sra-pileup --version</version_string>
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17 <inputs>
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18 <conditional name="input">
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19 <param name="input_select" type="select" label="select input type">
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20 <option value="accession_number">SRR accession</option>
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21 <option value="file">SRA archive in current history</option>
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22 </param>
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23 <when value="file">
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24 <param format="sra" name="file" type="data" label="sra archive"/>
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25 </when>
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26 <when value="accession_number">
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27 <param format="text" name="accession" type="text" label="accession"/>
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28 </when>
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29 </conditional>
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30 <param format="text" name="region" type="text" label="aligned region"/>
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31 <param format="text" name="minMapq" type="text" label="minimum mapping quality"/>
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32 </inputs>
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33 <outputs>
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34 <data format="pileup" name="output"/>
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35 </outputs>
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36 <requirements>
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37 <requirement type="package" version="2.3.2-4">sra_toolkit</requirement>
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38 </requirements>
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39 <help>
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40 This tool produces pileup format from sra archives using sra-pileup.
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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.
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42 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
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43 </help>
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44 </tool>