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annotate sra_macros.xml @ 0:9f74a22d2060 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
author mvdbeek
date Wed, 04 Nov 2015 06:57:32 -0500
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9f74a22d2060 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
mvdbeek
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1 <macros>
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2 <macro name="requirements">
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3 <requirements>
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4 <requirement type="package" version="1.1.3">ngs_sdk</requirement>
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5 <requirement type="package" version="2.5.2">ncbi_vdb</requirement>
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6 <requirement type="package" version="2.5.2">sra_toolkit</requirement>
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7 <requirement type="package" version="3">ascp</requirement>
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8 <requirement type="package" version="5.18.1">perl</requirement>
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9 </requirements>
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10 </macro>
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11 <macro name="input_conditional">
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12 <conditional name="input">
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13 <param name="input_select" type="select" label="select input type">
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14 <option value="accession_number">SRR accession</option>
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15 <option value="file">SRA archive in current history</option>
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16 </param>
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17 <when value="accession_number">
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18 <param name="accession" type="text" label="accession"/>
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19 </when>
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20 <when value="file">
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21 <param format="sra" name="file" type="data" label="sra archive"/>
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22 </when>
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23 </conditional>
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24 </macro>
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25 <macro name="alignments">
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26 <param name="alignments" type="select" value="both">
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27 <label>aligned or unaligned reads</label>
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28 <option value="both">both</option>
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29 <option value="aligned">aligned only</option>
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30 <option value="unaligned">unaligned only</option>
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31 </param>
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32 </macro>
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33 <macro name="minMapq">
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34 <param name="minMapq" type="integer" min="0" max="42" label="minimum mapping quality" optional="true"/>
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35 </macro>
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36 <macro name="region">
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37 <param format="text" name="region" type="text" label="aligned region" optional="true"
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38 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"/>
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39 </macro>
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40 <macro name="matepairDist">
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41 <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true"
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42 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"/>
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43 </macro>
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44 <token name="@SRATOOLS_ATTRRIBUTION@">Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
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45 Galaxy tool wrapper originally written by Matt Shirley (mdshw5 at gmail.com).
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46 Tool dependencies, clean-up and bug-fixes by Marius van den Beek (m.vandenbeek at gmail.com).
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47 For support and bug reports contact Matt Shirley or Marius van den Beek or go to https://github.com/mdshw5/sra-tools-galaxy.</token>
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48 </macros>