Mercurial > repos > iuc > data_manager_mothur_toolsuite

annotate data_manager/data_manager_fetch_mothur_reference_data.xml @ 0:ab7a7e798c34 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
author iuc
date Mon, 06 Nov 2017 06:21:50 -0500
parents
children aec831b54a5b
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ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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1 <?xml version="1.0"?>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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2 <tool id="data_manager_fetch_mothur_reference_data" name="Fetch Mothur toolsuite reference data" version="0.1.3" tool_type="manage_data">
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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3 <description>Fetch and install reference data for Mothur</description>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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4 <requirements>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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5 <requirement type="package" version="2.7">python</requirement>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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6 </requirements>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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7 <command><![CDATA[
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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8 python '$__tool_directory__/fetch_mothur_reference_data.py'
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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9 --source=$data_source.data_source_selector
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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10 #if str( $data_source.data_source_selector ) == "mothur_website"
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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11 --datasets '${data_source.ref_data}'
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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12 #elif str( $data_source.data_source_selector ) == "filesystem_paths"
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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13 --description '${data_source.description}'
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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14 --paths '${data_source.paths}'
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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15 #if $data_source.create_symlink
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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16 --link
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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17 #end if
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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18 #end if
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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19 '${out_file}'
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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20 ]]></command>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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21 <inputs>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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22 <conditional name="data_source">
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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23 <param name="data_source_selector" type="select"
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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24 label="Choose the source for the reference data">
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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25 <option value="mothur_website">Mothur website</option>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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26 <option value="filesystem_paths">Filesystem paths</option>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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27 </param>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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28 <when value="mothur_website">
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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29 <param name="ref_data" type="select" display="checkboxes" multiple="true"
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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30 label="Reference dataset to install">
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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31 <option value="lookup_titanium">GS FLX Titanium lookup files</option>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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32 <option value="lookup_gsflx">GSFLX lookup files</option>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
iuc
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33 <option value="lookup_gs20">GS20 lookup files</option>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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34 <option value="RDP_v16">RDP reference files (training set version 16)</option>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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35 <option value="RDP_v14">RDP reference files (training set version 14)</option>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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36 <option value="RDP_v10">RDP reference files (training set version 10)</option>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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37 <option value="RDP_v9">RDP reference files (training set version 9)</option>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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38 <option value="RDP_v7">RDP reference files (training set version 7)</option>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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39 <option value="RDP_v6">RDP reference files (training set version 6)</option>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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40 <option value="silva_release_128">SILVA reference files (release 128)</option>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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41 <option value="silva_release_123">SILVA reference files (release 123)</option>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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42 <option value="silva_release_119">SILVA reference files (release 119)</option>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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43 <option value="silva_release_102">SILVA reference files (release 102)</option>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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44 <option value="greengenes_August2013">Greengenes reference taxonomy and alignment v13.8 (August 2013)</option>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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45 <option value="greengenes_May2013">Greengenes reference taxonomy and alignment v13.5 (May 2013)</option>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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46 <option value="greengenes_old">Greengenes reference taxonomy and alignment (pre-May 2013)</option>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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47 <option value="greengenes_gold_alignment">Greengenes gold alignment</option>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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48 <option value="secondary_structure_maps_silva">SILVA secondary structure maps</option>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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49 <option value="secondary_structure_maps_greengenes">Greengenes secondary structure maps</option>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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50 </param>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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51 </when>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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52 <when value="filesystem_paths">
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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53 <param name="description" type="text" value="" size="50"
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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54 label="Description of the data" optional="False" />
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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55 <param name="paths" type="text" value="" area="True" size="10x50"
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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56 label="Paths to upload" optional="False"
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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57 help="Upload all files pasted in the box. The (recursive) contents of any pasted directories will be added as well." />
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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58 <param type="boolean" name="create_symlink" truevalue="create_symlink"
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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59 falsevalue="copy_file"
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60 label="Create symlinks to data instead of copying into Galaxy" checked="on" />
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61 </when>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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62 </conditional>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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63 </inputs>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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64 <outputs>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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65 <data name="out_file" format="data_manager_json" />
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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66 </outputs>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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67 <tests>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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68 <test>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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69 <param name="data_sourece|ref_data" value="lookup_titanium"/>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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70 <output name="out_file">
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71 <assert_contents>
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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72 <has_text text="GS FLX Titanium" />
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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73 <has_text text="LookUp_Titanium.pat" />
ab7a7e798c34 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea
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74 </assert_contents>
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75 </output>
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76 </test>
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77 </tests>
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78 <help>
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79 .. class:: infomark
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80
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81 **What it does**
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82
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83 This tool fetches reference data used by the mothur_toolsuite set of Galaxy tools,
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84 and populates the appropriate data tables.
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85
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86 The reference data can be imported directly from the Mothur website, or from files
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87 in a server directory.
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88
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89 Files are added to the following data tables based on file extension:
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90
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91 * **mothur_lookup**: for .pat files
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92 * **mothur_aligndb**: for .fasta files
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93 * **mothur_map**: for .map files
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94 * **mothur_taxonomy**: for .tax files
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95
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96 ------
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97
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98 **Importing from Mothur website**
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99
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100 Reference data sets provided by the Mothur developers can be downloaded from the
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101 Mothur website. See the following pages to get more information about each dataset:
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102
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103 * Lookup data: http://www.mothur.org/wiki/Lookup_files
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104 * RDP reference data: http://www.mothur.org/wiki/RDP_reference_files
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105 * Silva data: http://www.mothur.org/wiki/Silva_reference_files
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106 * Greengenes data: http://www.mothur.org/wiki/Greengenes-formatted_databases
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107 * Secondary structure maps: http://www.mothur.org/wiki/Secondary_structure_map
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108
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109 **Importing from file system paths**
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110
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111 If reference data is already on the server filesystem then use this option to
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112 import it into the Mothur data tables. The appropriate data tables are determined
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113 based on the file extensions.
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114
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115 Optionally a description can be added which will appear next to the base of the
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116 reference file name in the data table entry.
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117
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118 ------
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119
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120 .. class:: warningmark
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121
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122 **A note on Lane masks**
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123
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124 Lane mask data is also available via the Mothur website (files ending in ".filter"):
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125
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126 * http://www.mothur.org/wiki/Lane_mask
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127
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128 but as these data are not currently used in the toolsuite, they cannot be imported
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129 using this data manager.
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130
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131 </help>
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132 </tool>