Mercurial > repos > matthias > data_manager_dada2
changeset 6:e374299894b0 draft
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(-) [+] |
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--- 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 & 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"}}} \ No newline at end of file