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comparison data_manager/dada2_fetcher.xml @ 6:5711fc06a63e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit 27be397d903081b2e7848e568c587917e4f49b89
author iuc
date Tue, 27 Jun 2023 17:26:40 +0000
parents 48a42ca61006
children 678176bff643
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5:48a42ca61006 6:5711fc06a63e
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="dada2_fetcher" name="dada2 data manager" tool_type="manage_data" version="0.0.8"> 2 <tool id="dada2_fetcher" name="dada2 data manager" tool_type="manage_data" version="0.1.0">
3 <description>Download reference databases</description>
3 <requirements> 4 <requirements>
4 <requirement type="package" version="3.7">python</requirement> 5 <requirement type="package" version="3.7">python</requirement>
5 </requirements> 6 </requirements>
6 <description>Download reference databases</description>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 python '$__tool_directory__/data_manager.py' 8 python '$__tool_directory__/data_manager.py'
9 --out '$out_file' 9 --out '$out_file'
10 #set dataset = str($db_cond.db_select) + '_' + str($db_cond.version_select) 10 #set dataset = str($db_cond.db_select) + '_' + str($db_cond.version_select)
11 --dataset '$dataset' 11 --dataset '$dataset'
141 .......................................................... 141 ..........................................................
142 142
143 The following refrence databases which are describes as maintained by the DADA2 project (https://benjjneb.github.io/dada2/training.html) are available 143 The following refrence databases which are describes as maintained by the DADA2 project (https://benjjneb.github.io/dada2/training.html) are available
144 144
145 - Silva (https://www.arb-silva.de/) 145 - Silva (https://www.arb-silva.de/)
146 - RDP (http://rdp.cme.msu.edu/) 146 - RDP
147 - GreenGenes (http://greengenes.secondgenome.com/) 147 - GreenGenes (http://greengenes.secondgenome.com/)
148 - UNITE general FASTA (https://unite.ut.ee/repository.php) 148 - UNITE general FASTA (https://unite.ut.ee/repository.php)
149 149
150 While Silva and RDP contain reference databases for taxonomy and species assignment, the greengenes and UNITE databases only contains a reference database for taxonomy assignment. 150 While Silva and RDP contain reference databases for taxonomy and species assignment, the greengenes and UNITE databases only contains a reference database for taxonomy assignment.
151 151
172 More detailed informations in the reference data bases can be found on the DADA2 website and contained links: https://benjjneb.github.io/dada2/training.html. 172 More detailed informations in the reference data bases can be found on the DADA2 website and contained links: https://benjjneb.github.io/dada2/training.html.
173 ]]></help> 173 ]]></help>
174 <citations> 174 <citations>
175 <!-- silva --> 175 <!-- silva -->
176 <citation type="doi">10.1093/nar/gks1219</citation> 176 <citation type="doi">10.1093/nar/gks1219</citation>
177 <!-- rdp -->> 177 <!-- rdp -->
178 <citation type="doi">10.1093/nar/gkt1244</citation> 178 <citation type="doi">10.1093/nar/gkt1244</citation>
179 <!-- greengenes --> 179 <!-- greengenes -->
180 <citation type="doi">10.1128/AEM.03006-05</citation> 180 <citation type="doi">10.1128/AEM.03006-05</citation>
181 <!-- unite --> 181 <!-- unite -->
182 <citation type="doi">10.15156/BIO/786343</citation> 182 <citation type="doi">10.15156/BIO/786343</citation>