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annotate sra_macros.xml @ 3:4732693f4661 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit f30369bef4e2cef17395cdd62ce81768c93f5edd
author iuc
date Tue, 18 Oct 2016 14:54:40 -0400
parents f256cb398262
children 62e4d56ebb6f
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1 <macros>
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2 <token name="@VERSION@">2.7.0</token>
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3 <macro name="requirements">
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4 <requirements>
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5 <requirement type="package" version="2.7.0">sra-tools</requirement>
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6 </requirements>
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7 </macro>
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8 <macro name="input_conditional">
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9 <conditional name="input">
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10 <param name="input_select" type="select" label="select input type">
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11 <option value="accession_number">SRR accession</option>
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12 <option value="file">SRA archive in current history</option>
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13 <option value="file_list">List of SRA accession, one per line</option>
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14 </param>
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15 <when value="accession_number">
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16 <param name="accession" type="text" label="SRR accession" help="Must start with SRR,DRR or ERR, e.g. SRR925743 , ERR343809"/>
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17 </when>
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18 <when value="file">
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19 <param format="sra" name="file" type="data" label="sra archive"/>
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20 </when>
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21 <when value="file_list">
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22 <param format="txt" name="file_list" type="data" label="sra accession list"/>
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23 </when>
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24 </conditional>
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25 </macro>
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26 <macro name="alignments">
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27 <param name="alignments" type="select" value="both">
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28 <label>aligned or unaligned reads</label>
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29 <option value="both">both</option>
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30 <option value="aligned">aligned only</option>
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31 <option value="unaligned">unaligned only</option>
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32 </param>
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33 </macro>
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34 <macro name="minMapq">
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35 <param name="minMapq" type="integer" min="0" max="42" label="minimum mapping quality" optional="true"/>
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36 </macro>
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37 <macro name="region">
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38 <param format="text" name="region" type="text" label="aligned region" optional="true"
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39 help="Filter by position on genome. Can be either accession.version (ex: NC_000001.10), chromosome name (ex:chr1 or 1) or 1-based coordinates (ex: chr1:1-101)."/>
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40 </macro>
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41 <macro name="matepairDist">
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42 <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true"
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43 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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44 </macro>
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45 <macro name="citation">
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46 <citations>
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47 <citation type="doi">10.1093/nar/gkq1019</citation>
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48 </citations>
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49 </macro>
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50 <token name="@SRATOOLS_ATTRRIBUTION@">
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51 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
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52
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53 Galaxy tool wrapper originally written by Matt Shirley (mdshw5 at gmail.com).
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54
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55 Wrapper modified by Philip Mabon ( philip.mabon at phac-aspc.gc.ca ).
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56
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57 Tool dependencies, clean-up and bug-fixes by Marius van den Beek (m.vandenbeek at gmail.com).
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58
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59 For support and bug reports contact Matt Shirley or Marius van den Beek or go to https://github.com/galaxyproject/tools-iuc.
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60
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61 </token>
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62 </macros>