Mercurial > repos > iuc > data_manager_dada2

changeset 2:a6a81f921701 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit a096d3eb593edee6cb08247be3a09138d088a6ce"
author iuc
date Sun, 29 Mar 2020 17:51:21 -0400
parents bf7b2c14cabc
children c29275496061
files data_manager/dada2_fetcher.xml data_manager/data_manager.py test-data/silva138_json
diffstat 3 files changed, 11 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/dada2_fetcher.xml	Thu Dec 05 17:58:52 2019 -0500
+++ b/data_manager/dada2_fetcher.xml	Sun Mar 29 17:51:21 2020 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="dada2_fetcher" name="dada2 data manager" tool_type="manage_data" profile="18.09" version="0.0.8">
+<tool id="dada2_fetcher" name="dada2 data manager" tool_type="manage_data" profile="18.09" version="0.0.9">
     <description>Download reference databases</description>
     <requirements>
         <requirement type="package" version="3.7">python</requirement>
@@ -27,6 +27,7 @@
             </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>
@@ -81,6 +82,11 @@
     <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	Thu Dec 05 17:58:52 2019 -0500
+++ b/data_manager/data_manager.py	Sun Mar 29 17:51:21 2020 -0400
@@ -11,6 +11,7 @@
 DEFAULT_TAXLEVELS = "Kingdom,Phylum,Class,Order,Family,Genus,Species"
 
 FILE2NAME = {
+    "silva_138": "Silva version 138",
     "silva_132": "Silva version 132",
     "silva_128": "Silva version 128",
     "rdp_16": "RDP trainset 16",
@@ -26,6 +27,7 @@
 }
 
 FILE2TAXURL = {
+    "silva_138": "https://zenodo.org/record/3731176/files/silva_nr_v138_train_set.fa.gz?download=1",
     "silva_132": "https://zenodo.org/record/1172783/files/silva_nr_v132_train_set.fa.gz?download=1",
     "silva_128": "https://zenodo.org/record/824551/files/silva_nr_v128_train_set.fa.gz?download=1",
     "rdp_16": "https://zenodo.org/record/801828/files/rdp_train_set_16.fa.gz?download=1",
@@ -41,6 +43,7 @@
 }
 
 FILE2SPECIESURL = {
+    "silva_138": "https://zenodo.org/record/3731176/files/silva_species_assignment_v138.fa.gz?download=1",
     "silva_132": "https://zenodo.org/record/1172783/files/silva_species_assignment_v132.fa.gz?download=1",
     "silva_128": "https://zenodo.org/record/824551/files/silva_species_assignment_v128.fa.gz?download=1",
     "rdp_16": "https://zenodo.org/record/801828/files/rdp_species_assignment_16.fa.gz?download=1",
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/silva138_json	Sun Mar 29 17:51:21 2020 -0400
@@ -0,0 +1,1 @@
+{"data_tables": {"dada2_species": {"name": "Silva version 138", "path": "silva_138.species", "value": "silva_138"}, "dada2_taxonomy": {"name": "Silva version 138", "path": "silva_138.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "silva_138"}}}
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