Mercurial > repos > iuc > data_manager_dada2

changeset 3:c29275496061 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit 8533fe71d1d50f09348da2dc34941724407a1ffe"
author iuc
date Tue, 14 Jul 2020 07:37:09 -0400
parents a6a81f921701
children 38ccd4589990
files data_manager/dada2_fetcher.xml data_manager/data_manager.py
diffstat 2 files changed, 5 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/dada2_fetcher.xml	Sun Mar 29 17:51:21 2020 -0400
+++ b/data_manager/dada2_fetcher.xml	Tue Jul 14 07:37:09 2020 -0400
@@ -1,9 +1,9 @@
 <?xml version="1.0"?>
-<tool id="dada2_fetcher" name="dada2 data manager" tool_type="manage_data" profile="18.09" version="0.0.9">
-    <description>Download reference databases</description>
+<tool id="dada2_fetcher" name="dada2 data manager" tool_type="manage_data" version="0.0.7">
     <requirements>
         <requirement type="package" version="3.7">python</requirement>
     </requirements>
+    <description>Download reference databases</description>
     <command detect_errors="exit_code"><![CDATA[
     python '$__tool_directory__/data_manager.py'
     --out '$out_file'
@@ -27,7 +27,6 @@
             </param>
             <when value="silva">
                 <param name="version_select" type="select" label="Database version">
-                    <option value="138">138</option>
                     <option value="132">132</option>
                     <option value="128">128</option>
                 </param>
@@ -82,11 +81,6 @@
     <tests>
         <test>
             <param name="db_cond|db_select" value="silva"/>
-            <param name="db_cond|version_select" value="138"/>
-            <output name="out_file" file="silva138_json"/>
-        </test>
-        <test>
-            <param name="db_cond|db_select" value="silva"/>
             <param name="db_cond|version_select" value="132"/>
             <output name="out_file" file="silva132_json"/>
         </test>
--- a/data_manager/data_manager.py	Sun Mar 29 17:51:21 2020 -0400
+++ b/data_manager/data_manager.py	Tue Jul 14 07:37:09 2020 -0400
@@ -105,7 +105,7 @@
 
     workdir = params['output_data'][0]['extra_files_path']
     os.mkdir(workdir)
-    url_download( FILE2TAXURL[dataset], dataset + ".taxonomy", workdir)
+    url_download(FILE2TAXURL[dataset], dataset + ".taxonomy", workdir)
 
     data_manager_json = {"data_tables": {}}
     data_manager_entry = {}
@@ -115,8 +115,8 @@
     data_manager_entry['taxlevels'] = FILE2TAXLEVELS.get(dataset, DEFAULT_TAXLEVELS)
     data_manager_json["data_tables"]["dada2_taxonomy"] = data_manager_entry
 
-    if FILE2SPECIESURL.get(dataset, False ):
-        url_download( FILE2SPECIESURL[dataset], dataset + ".species", workdir)
+    if FILE2SPECIESURL.get(dataset, False):
+        url_download(FILE2SPECIESURL[dataset], dataset + ".species", workdir)
         data_manager_entry = {}
         data_manager_entry['value'] = dataset
         data_manager_entry['name'] = FILE2NAME[dataset]