Mercurial > repos > matthias > data_manager_dada2

changeset 6:e374299894b0 draft

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 11ea529bf7414a4a20e414b50ce7cee5cb5dc4c4
author matthias
date Thu, 06 Jun 2019 07:59:19 -0400
parents b899349a9c2b
children 42bbbc4b4739
files data_manager/.dada2_fetcher.xml.swp data_manager/.data_manager.py.swp data_manager/dada2_fetcher.xml test-data/dada2_species.loc test-data/dada2_taxonomy.loc test-data/unite8fungisingletons_json
diffstat 6 files changed, 8 insertions(+), 17 deletions(-) [+]
line wrap: on
line diff
Binary file data_manager/.dada2_fetcher.xml.swp has changed
Binary file data_manager/.data_manager.py.swp has changed
--- a/data_manager/dada2_fetcher.xml	Fri May 10 11:54:21 2019 -0400
+++ b/data_manager/dada2_fetcher.xml	Thu Jun 06 07:59:19 2019 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="dada_fetcher" name="dada2 data manager" tool_type="manage_data" version="0.0.6">
+<tool id="dada_fetcher" name="dada2 data manager" tool_type="manage_data" version="0.0.7">
     <description>Download reference databases</description>
     <command detect_errors="exit_code"><![CDATA[
     python '$__tool_directory__/data_manager.py'
@@ -41,7 +41,7 @@
             <when value="unite">
                 <param name="version_select" type="select" label="Database version">
                     <option value="8.0_fungi">release 8.0 for Fungi</option>
-                    <option value="8.0_fungi_singleton">release 8.0 for Fungi including global and 97% singletons</option>
+                    <option value="8.0_fungi_singletons">release 8.0 for Fungi including global and 97% singletons</option>
                 </param>
             </when>
             <when value="RefSeq_RDP">
@@ -96,6 +96,11 @@
             <output name="out_file" file="unite8fungi_json"/>
         </test>
         <test>
+            <param name="db_cond|db_select" value="unite"/>
+            <param name="db_cond|version_select" value="8.0_fungi_singletons"/>
+            <output name="out_file" file="unite8fungisingletons_json"/>
+        </test>
+        <test>
             <param name="db_cond|db_select" value="RefSeq_RDP"/>
             <param name="db_cond|version_select" value="2018_05"/>
             <output name="out_file" file="RefSeq_RDP2018_json"/>
--- a/test-data/dada2_species.loc	Fri May 10 11:54:21 2019 -0400
+++ b/test-data/dada2_species.loc	Thu Jun 06 07:59:19 2019 -0400
@@ -7,7 +7,3 @@
 # Datasets can be retrieved from http://busco.ezlab.org/frame_wget.html
 #
 # Datasets can be retrieved from https://benjjneb.github.io/dada2/training.html
-silva_132	Silva version 132	/tmp/tmpC8Yc3F/tmpzwAZwA/tmpZp3_e0/database/data_manager_tool-datal4tFOr/dada2/silva_132.species
-rdp_16	RDP trainset 16	/tmp/tmpC8Yc3F/tmpzwAZwA/tmpZp3_e0/database/data_manager_tool-datal4tFOr/dada2/rdp_16.species
-rdp_16	RDP trainset 16	/tmp/tmpLsjmNt/tmppH8mTW/tmpqUnkc6/database/data_manager_tool-data1EI7iU/dada2/rdp_16.species
-silva_132	Silva version 132	/tmp/tmpLsjmNt/tmppH8mTW/tmpqUnkc6/database/data_manager_tool-data1EI7iU/dada2/silva_132.species
--- a/test-data/dada2_taxonomy.loc	Fri May 10 11:54:21 2019 -0400
+++ b/test-data/dada2_taxonomy.loc	Thu Jun 06 07:59:19 2019 -0400
@@ -7,14 +7,3 @@
 # Datasets can be retrieved from https://benjjneb.github.io/dada2/training.html
 # 
 # taxlevels is a comma separated list of taxonomy levels
-silva_132	Silva version 132	/tmp/tmpC8Yc3F/tmpzwAZwA/tmpZp3_e0/database/data_manager_tool-datal4tFOr/dada2/silva_132.taxonomy	Kingdom,Phylum,Class,Order,Family,Genus,Species
-rdp_16	RDP trainset 16	/tmp/tmpC8Yc3F/tmpzwAZwA/tmpZp3_e0/database/data_manager_tool-datal4tFOr/dada2/rdp_16.taxonomy	Kingdom,Phylum,Class,Order,Family,Genus,Species
-greengenes_13.84	GreenGenes version 13.84	/tmp/tmpC8Yc3F/tmpzwAZwA/tmpZp3_e0/database/data_manager_tool-datal4tFOr/dada2/greengenes_13.84.taxonomy	Kingdom,Phylum,Class,Order,Family,Genus,Species
-unite_8.0_fungi	UNITE: General Fasta release 8.0 for Fungi	/tmp/tmpC8Yc3F/tmpzwAZwA/tmpZp3_e0/database/data_manager_tool-datal4tFOr/dada2/unite_8.0_fungi.taxonomy	Kingdom,Phylum,Class,Order,Family,Genus,Species
-RefSeq_RDP_2018_05	NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018)	/tmp/tmpC8Yc3F/tmpzwAZwA/tmpZp3_e0/database/data_manager_tool-datal4tFOr/dada2/RefSeq_RDP_2018_05.taxonomy	Kingdom,Phylum,Class,Order,Family,Genus,Species
-gtdb_2018_11	GTDB: Genome Taxonomy Database (Bacteria &amp; Archaea) (11/2018)	/tmp/tmpC8Yc3F/tmpzwAZwA/tmpZp3_e0/database/data_manager_tool-datal4tFOr/dada2/gtdb_2018_11.taxonomy	Kingdom,Phylum,Class,Order,Family,Genus,Species
-hitdb_1	HitDB version 1 (Human InTestinal 16S rRNA)	/tmp/tmpC8Yc3F/tmpzwAZwA/tmpZp3_e0/database/data_manager_tool-datal4tFOr/dada2/hitdb_1.taxonomy	Kingdom,Phylum,Class,Order,Family,Genus,Species
-silva_euk_18S_132	Silva version 132 Eukaryotic 18S	/tmp/tmpC8Yc3F/tmpzwAZwA/tmpZp3_e0/database/data_manager_tool-datal4tFOr/dada2/silva_euk_18S_132.taxonomy	Kingdom,Phylum,Class,Order,Family,Genus,Species
-PR2_4.11.1	Protist Ribosomal Reference database (PR2) 4.11.1	/tmp/tmpC8Yc3F/tmpzwAZwA/tmpZp3_e0/database/data_manager_tool-datal4tFOr/dada2/PR2_4.11.1.taxonomy	Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species
-rdp_16	RDP trainset 16	/tmp/tmpLsjmNt/tmppH8mTW/tmpqUnkc6/database/data_manager_tool-data1EI7iU/dada2/rdp_16.taxonomy	Kingdom,Phylum,Class,Order,Family,Genus,Species
-silva_132	Silva version 132	/tmp/tmpLsjmNt/tmppH8mTW/tmpqUnkc6/database/data_manager_tool-data1EI7iU/dada2/silva_132.taxonomy	Kingdom,Phylum,Class,Order,Family,Genus,Species
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/unite8fungisingletons_json	Thu Jun 06 07:59:19 2019 -0400
@@ -0,0 +1,1 @@
+{"data_tables": {"dada2_taxonomy": {"path": "unite_8.0_fungi_singletons.taxonomy", "name": "UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons", "value": "unite_8.0_fungi_singletons", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species"}}}
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