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annotate sra_tools-04cc8176e86f/sra_pileup.xml @ 0:c386fe82db82

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Initial commit, moving from test tool shed.
author matt-shirley
date Wed, 25 Sep 2013 21:00:05 -0400
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1 <tool id="sra_pileup" name="Generate pileup format" version="1.1.1">
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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 #elif $input.input_select == "accession_number":
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13 $input.accession
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14 #elif $input.input_select == "text":
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15 `cat $input.text`
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16 #end if
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17 > $output</command>
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18 <version_string>sra-pileup --version</version_string>
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19 <inputs>
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20 <conditional name="input">
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21 <param name="input_select" type="select" label="select input type">
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22 <option value="accession_number">SRR accession</option>
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23 <option value="file">SRA archive in current history</option>
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24 <option value="text">text file containing SRR accession</option>
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25 </param>
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26 <when value="file">
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27 <param format="sra" name="file" type="data" label="sra archive"/>
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28 </when>
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29 <when value="accession_number">
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30 <param format="text" name="accession" type="text" label="accession"/>
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31 </when>
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32 <when value="text">
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33 <param format="txt" name="text" type="data" label="text file"/>
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34 </when>
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35 </conditional>
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36 <param format="text" name="region" type="text" label="aligned region"/>
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37 <param format="text" name="minMapq" type="text" label="minimum mapping quality"/>
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38 </inputs>
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39 <outputs>
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40 <data format="pileup" name="output"/>
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41 </outputs>
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42 <requirements>
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43 <requirement type="package" version="2.3.3-3">sra_toolkit</requirement>
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44 </requirements>
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45 <help>
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46 This tool produces pileup format from sra archives using sra-pileup.
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47 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
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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.
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49 Contact Matt Shirley at mdshw5@gmail.com for support and bug reports.
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50 </help>
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51 </tool>