Mercurial > repos > iuc > data_manager_mothur_toolsuite

comparison data_manager/data_manager_fetch_mothur_reference_data.xml @ 4:0db22932bc39 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e"
author iuc
date Fri, 25 Jun 2021 09:37:05 +0000
parents 0e532fc0a0a6
children f21e77139fb5
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3:9d09724f2bf1 4:0db22932bc39
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="data_manager_fetch_mothur_reference_data" name="Fetch Mothur toolsuite reference data" version="0.1.5" tool_type="manage_data" profile="19.05"> 2 <tool id="data_manager_fetch_mothur_reference_data" name="Fetch Mothur toolsuite reference data" version="0.2.1" tool_type="manage_data" profile="19.05">
3 <description>Fetch and install reference data for Mothur</description> 3 <description>Fetch and install reference data for Mothur</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2.7">python</requirement> 5 <requirement type="package" version="3.8">python</requirement>
6 </requirements> 6 </requirements>
7 <command><![CDATA[ 7 <command><![CDATA[
8 python '$__tool_directory__/fetch_mothur_reference_data.py' 8 python '$__tool_directory__/fetch_mothur_reference_data.py'
9 --source=$data_source.data_source_selector 9 --source=$data_source.data_source_selector
10 #if str( $data_source.data_source_selector ) == "mothur_website" 10 #if str( $data_source.data_source_selector ) == "mothur_website"
29 <param name="ref_data" type="select" display="checkboxes" multiple="true" 29 <param name="ref_data" type="select" display="checkboxes" multiple="true"
30 label="Reference dataset to install"> 30 label="Reference dataset to install">
31 <option value="lookup_titanium">GS FLX Titanium lookup files</option> 31 <option value="lookup_titanium">GS FLX Titanium lookup files</option>
32 <option value="lookup_gsflx">GSFLX lookup files</option> 32 <option value="lookup_gsflx">GSFLX lookup files</option>
33 <option value="lookup_gs20">GS20 lookup files</option> 33 <option value="lookup_gs20">GS20 lookup files</option>
34 <option value="RDP_v18">RDP reference files (training set version 18)</option>
34 <option value="RDP_v16">RDP reference files (training set version 16)</option> 35 <option value="RDP_v16">RDP reference files (training set version 16)</option>
35 <option value="RDP_v14">RDP reference files (training set version 14)</option> 36 <option value="RDP_v14">RDP reference files (training set version 14)</option>
36 <option value="RDP_v10">RDP reference files (training set version 10)</option> 37 <option value="RDP_v10">RDP reference files (training set version 10)</option>
37 <option value="RDP_v9">RDP reference files (training set version 9)</option> 38 <option value="RDP_v9">RDP reference files (training set version 9)</option>
38 <option value="RDP_v7">RDP reference files (training set version 7)</option> 39 <option value="RDP_v7">RDP reference files (training set version 7)</option>
39 <option value="RDP_v6">RDP reference files (training set version 6)</option> 40 <option value="RDP_v6">RDP reference files (training set version 6)</option>
41 <option value="silva_release_138.1">SILVA reference files (release 138.1)</option>
40 <option value="silva_release_128">SILVA reference files (release 128)</option> 42 <option value="silva_release_128">SILVA reference files (release 128)</option>
41 <option value="silva_release_123">SILVA reference files (release 123)</option> 43 <option value="silva_release_123">SILVA reference files (release 123)</option>
42 <option value="silva_release_119">SILVA reference files (release 119)</option> 44 <option value="silva_release_119">SILVA reference files (release 119)</option>
43 <option value="silva_release_102">SILVA reference files (release 102)</option> 45 <option value="silva_release_102">SILVA reference files (release 102)</option>
44 <option value="greengenes_August2013">Greengenes reference taxonomy and alignment v13.8 (August 2013)</option> 46 <option value="greengenes_August2013">Greengenes reference taxonomy and alignment v13.8 (August 2013)</option>
91 <has_text text="LookUp_GS20.pat" /> 93 <has_text text="LookUp_GS20.pat" />
92 </assert_contents> 94 </assert_contents>
93 </output> 95 </output>
94 </test> 96 </test>
95 <test> 97 <test>
98 <param name="data_source|ref_data" value="RDP_v18"/>
99 <output name="out_file">
100 <assert_contents>
101 <has_text text="16S rRNA RDP training set 18" />
102 <has_text text="trainset18_062020.rdp.fasta" />
103 <has_text text="trainset18_062020.rdp.tax" />
104 <has_text text="trainset18_062020.pds.fasta" />
105 <has_text text="trainset18_062020.pds.tax" />
106 </assert_contents>
107 </output>
108 </test>
109 <test>
96 <param name="data_source|ref_data" value="RDP_v16"/> 110 <param name="data_source|ref_data" value="RDP_v16"/>
97 <output name="out_file"> 111 <output name="out_file">
98 <assert_contents> 112 <assert_contents>
99 <has_text text="16S rRNA RDP training set 16" /> 113 <has_text text="16S rRNA RDP training set 16" />
100 <has_text text="trainset16_022016.rdp.fasta" /> 114 <has_text text="trainset16_022016.rdp.fasta" />