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annotate sra_macros.xml @ 3:d77993393d0a draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 4abfa4aaee08afe2a3246420ce5d131e1c1d42d8-dirty
author mvdbeek
date Fri, 25 Sep 2015 12:27:31 -0400
parents 68527898a9ea
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68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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1 <macros>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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2 <macro name="requirements">
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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3 <requirements>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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4 <requirement type="package" version="2.5.2">sra_toolkit</requirement>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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5 <requirement type="package" version="3">ascp</requirement>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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6 <requirement type="package" version="5.18.1">perl</requirement>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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7 </requirements>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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8 </macro>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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9 <macro name="input_conditional">
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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10 <conditional name="input">
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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11 <param name="input_select" type="select" label="select input type">
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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12 <option value="accession_number">SRR accession</option>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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13 <option value="file">SRA archive in current history</option>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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14 </param>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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15 <when value="accession_number">
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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16 <param name="accession" type="text" label="accession"/>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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17 </when>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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18 <when value="file">
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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19 <param format="sra" name="file" type="data" label="sra archive"/>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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20 </when>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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21 </conditional>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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22 </macro>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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23 <macro name="alignments">
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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24 <param name="alignments" type="select" value="both">
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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25 <label>aligned or unaligned reads</label>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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26 <option value="both">both</option>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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27 <option value="aligned">aligned only</option>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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28 <option value="unaligned">unaligned only</option>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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29 </param>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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30 </macro>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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31 <macro name="minMapq">
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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32 <param name="minMapq" type="integer" min="0" max="42" label="minimum mapping quality" optional="true"/>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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33 </macro>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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34 <macro name="region">
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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35 <param format="text" name="region" type="text" label="aligned region" optional="true"
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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36 help="Filter by position on genome. Name can either be accession.version (ex: NC_000001.10) or file specific name (ex:chr1 or 1). from and to are 1-based coordinates"/>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
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37 </macro>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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38 <macro name="matepairDist">
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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39 <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true"
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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40 help="Filter by distance between matepairs. Use unknown to find matepairs split between the references. Use from-to (inclusive) to limit matepair distance on the same reference"/>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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41 </macro>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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42 <token name="@SRATOOLS_ATTRRIBUTION@">Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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43 Galaxy tool wrapper originally written by Matt Shirley (mdshw5 at gmail.com).
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
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44 Tool dependencies, clean-up and bug-fixes by Marius van den Beek (m.vandenbeek at gmail.com).
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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45 For support and bug reports contact Matt Shirley or Marius van den Beek or go to https://github.com/mdshw5/sra-tools-galaxy.</token>
68527898a9ea planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
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46 </macros>