Mercurial > repos > matthias > data_manager_dada2

diff data_manager/dada2_fetcher.xml @ 1:1c50cfb0c0ab draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 42eb67646e47bef13eed672ff6b9d06b1d82ae3d-dirty
author matthias
date Thu, 07 Mar 2019 11:48:18 -0500
parents
children b4c303665291
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/dada2_fetcher.xml	Thu Mar 07 11:48:18 2019 -0500
@@ -0,0 +1,39 @@
+<?xml version="1.0"?>
+<tool id="dada_fetcher" name="dada2 dada manager" tool_type="manage_data" version="0.0.2">
+    <description>Download reference data sets</description>
+    <command detect_errors="exit_code">
+    <![CDATA[
+    python '$__tool_directory__/data_manager.py' 
+    --out '${out_file}'
+    --file '$type_cond.database_name'
+    ]]>
+    </command>
+    <inputs>
+        <param name="database_name" type="select" label="mapping data">
+            <option value="silva132">Silva version 132</option>
+            <option value="silva128">Silva version 128</option>
+            <option value="rdp16">RDP trainset 16 + RDP database release 11.5</option>
+            <option value="rdp14">RDP trainset 14</option>
+            <option value="gg13.84">GreenGenes version 13.8</option>
+<!--            <option value="unite8.0">UNITE: General Fasta release 8.0 </option>
+            <option value="RefSeq_RDP">NCBI RefSeq 16S rRNA database supplemented by RDP</option>
+            <option value="gtdb">GTDB: Genome Taxonomy Database (More info: http://gtdb.ecogenomic.org/)</option>
+            <option value="hitdb1">HitDB version 1 (Human InTestinal 16S rRNA)</option>
+            <option value="silva132_euk">Silva Eukaryotic 18S, v132 &amp; v128</option>
+            <option value="PR2v4.11.0">Protist Ribosomal Reference database 2 version 4.11.0</option>-->
+        </param>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="database_name" value="silva132"/>
+            <output name="out_file" file="silva132_json"/>
+        </test>
+    </tests>
+    <help>
+http://www.arb-silva.de/silva-license-information
+    </help>
+</tool>
+