| Previous changeset 3:3a4ee8bf012a (2019-04-09) Next changeset 5:b899349a9c2b (2019-05-10) |
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Commit message:
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/data_managers/data_manager_dada2 commit 2f47c03d1b775ab796c75c806c1ab247bb51359d |
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modified:
data_manager/dada2_fetcher.xml |
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added:
data_manager/.dada2_fetcher.xml.swp data_manager/.data_manager.py.swp test-data/PR24.11.1_json test-data/RefSeq_RDP2018_json test-data/dada2_species.loc test-data/dada2_taxonomy.loc test-data/greengenes13.84_json test-data/gtdb2018_json test-data/hitdb1_json test-data/rdp16_json test-data/silva132_json test-data/silvaeuk132_json test-data/unite8fungi_json tool_data_table_conf.xml.test |
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removed:
data_manager/test-data/PR24.11.1_json data_manager/test-data/RefSeq_RDP2018_json data_manager/test-data/greengenes13.84_json data_manager/test-data/gtdb2018_json data_manager/test-data/hitdb1_json data_manager/test-data/rdp16_json data_manager/test-data/silva132_json data_manager/test-data/silvaeuk132_json data_manager/test-data/unite8fungi_json |
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| diff -r 3a4ee8bf012a -r 51b90d282704 data_manager/.dada2_fetcher.xml.swp |
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| Binary file data_manager/.dada2_fetcher.xml.swp has changed |
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| diff -r 3a4ee8bf012a -r 51b90d282704 data_manager/.data_manager.py.swp |
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| Binary file data_manager/.data_manager.py.swp has changed |
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| diff -r 3a4ee8bf012a -r 51b90d282704 data_manager/dada2_fetcher.xml --- a/data_manager/dada2_fetcher.xml Tue Apr 09 07:18:57 2019 -0400 +++ b/data_manager/dada2_fetcher.xml Fri May 10 11:52:03 2019 -0400 |
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| @@ -1,10 +1,11 @@ <?xml version="1.0"?> -<tool id="dada_fetcher" name="dada2 data manager" version="0.0.5"> +<tool id="dada_fetcher" name="dada2 data manager" tool_type="manage_data" version="0.0.5"> <description>Download reference databases</description> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/data_manager.py' - --out '${out_file}' - --dataset '$db_cond.db_select'_'$db_cond.version_select' + --out '$out_file' + #set dataset = str($db_cond.db_select) + '_' + str($db_cond.version_select) + --dataset '$dataset' ]]> </command> <inputs> @@ -76,47 +77,47 @@ <tests> <test> <param name="db_cond|db_select" value="silva"/> - <param name="db_cond|db_version" value="132"/> + <param name="db_cond|version_select" value="132"/> <output name="out_file" file="silva132_json"/> </test> <test> <param name="db_cond|db_select" value="rdp"/> - <param name="db_cond|db_version" value="16"/> + <param name="db_cond|version_select" value="16"/> <output name="out_file" file="rdp16_json"/> </test> <test> <param name="db_cond|db_select" value="greengenes"/> - <param name="db_cond|db_version" value="13.84"/> + <param name="db_cond|version_select" value="13.84"/> <output name="out_file" file="greengenes13.84_json"/> </test> <test> <param name="db_cond|db_select" value="unite"/> - <param name="db_cond|db_version" value="8.0_fungi"/> + <param name="db_cond|version_select" value="8.0_fungi"/> <output name="out_file" file="unite8fungi_json"/> </test> <test> <param name="db_cond|db_select" value="RefSeq_RDP"/> - <param name="db_cond|db_version" value="2018_05"/> + <param name="db_cond|version_select" value="2018_05"/> <output name="out_file" file="RefSeq_RDP2018_json"/> </test> <test> <param name="db_cond|db_select" value="gtdb"/> - <param name="db_cond|db_version" value="2018_11"/> + <param name="db_cond|version_select" value="2018_11"/> <output name="out_file" file="gtdb2018_json"/> </test> <test> <param name="db_cond|db_select" value="hitdb"/> - <param name="db_cond|db_version" value="1"/> + <param name="db_cond|version_select" value="1"/> <output name="out_file" file="hitdb1_json"/> </test> <test> <param name="db_cond|db_select" value="silva_euk_18S"/> - <param name="db_cond|db_version" value="132"/> + <param name="db_cond|version_select" value="132"/> <output name="out_file" file="silvaeuk132_json"/> </test> <test> <param name="db_cond|db_select" value="PR2"/> - <param name="db_cond|db_version" value="4.11.1"/> + <param name="db_cond|version_select" value="4.11.1"/> <output name="out_file" file="PR24.11.1_json"/> </test> </tests> |
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| diff -r 3a4ee8bf012a -r 51b90d282704 data_manager/test-data/PR24.11.1_json --- a/data_manager/test-data/PR24.11.1_json Tue Apr 09 07:18:57 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -{"data_tables": {"dada2_taxonomy": {"path": "PR2_4.11.1.taxonomy", "name": "Protist Ribosomal Reference database (PR2) 4.11.1", "value": "PR2_4.11.1", "taxlevels": "Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species"}}} \ No newline at end of file |
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| diff -r 3a4ee8bf012a -r 51b90d282704 data_manager/test-data/RefSeq_RDP2018_json --- a/data_manager/test-data/RefSeq_RDP2018_json Tue Apr 09 07:18:57 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -{"data_tables": {"dada2_taxonomy": {"path": "RefSeq_RDP_2018_05.taxonomy", "name": "NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018)", "value": "RefSeq_RDP_2018_05", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species"}}} \ No newline at end of file |
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| diff -r 3a4ee8bf012a -r 51b90d282704 data_manager/test-data/greengenes13.84_json --- a/data_manager/test-data/greengenes13.84_json Tue Apr 09 07:18:57 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -{"data_tables": {"dada2_taxonomy": {"path": "greengenes_13.84.taxonomy", "name": "GreenGenes version 13.84", "value": "greengenes_13.84", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species"}}} \ No newline at end of file |
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| diff -r 3a4ee8bf012a -r 51b90d282704 data_manager/test-data/gtdb2018_json --- a/data_manager/test-data/gtdb2018_json Tue Apr 09 07:18:57 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -{"data_tables": {"dada2_taxonomy": {"path": "gtdb_2018_11.taxonomy", "name": "GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018)", "value": "gtdb_2018_11", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species"}}} \ No newline at end of file |
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| diff -r 3a4ee8bf012a -r 51b90d282704 data_manager/test-data/hitdb1_json --- a/data_manager/test-data/hitdb1_json Tue Apr 09 07:18:57 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -{"data_tables": {"dada2_taxonomy": {"path": "hitdb_1.taxonomy", "name": "HitDB version 1 (Human InTestinal 16S rRNA)", "value": "hitdb_1", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species"}}} \ No newline at end of file |
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| diff -r 3a4ee8bf012a -r 51b90d282704 data_manager/test-data/rdp16_json --- a/data_manager/test-data/rdp16_json Tue Apr 09 07:18:57 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -{"data_tables": {"dada2_species": {"path": "rdp_16.species", "name": "RDP trainset 16", "value": "rdp_16"}, "dada2_taxonomy": {"path": "rdp_16.taxonomy", "name": "RDP trainset 16", "value": "rdp_16", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species"}}} \ No newline at end of file |
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| diff -r 3a4ee8bf012a -r 51b90d282704 data_manager/test-data/silva132_json --- a/data_manager/test-data/silva132_json Tue Apr 09 07:18:57 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -{"data_tables": {"dada2_species": {"path": "silva_132.species", "name": "Silva version 132", "value": "silva_132"}, "dada2_taxonomy": {"path": "silva_132.taxonomy", "name": "Silva version 132", "value": "silva_132", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species"}}} \ No newline at end of file |
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| diff -r 3a4ee8bf012a -r 51b90d282704 data_manager/test-data/silvaeuk132_json --- a/data_manager/test-data/silvaeuk132_json Tue Apr 09 07:18:57 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -{"data_tables": {"dada2_taxonomy": {"path": "silva_euk_18S_132.taxonomy", "name": "Silva version 132 Eukaryotic 18S", "value": "silva_euk_18S_132", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species"}}} \ No newline at end of file |
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| diff -r 3a4ee8bf012a -r 51b90d282704 data_manager/test-data/unite8fungi_json --- a/data_manager/test-data/unite8fungi_json Tue Apr 09 07:18:57 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -{"data_tables": {"dada2_taxonomy": {"path": "unite_8.0_fungi.taxonomy", "name": "UNITE: General Fasta release 8.0 for Fungi", "value": "unite_8.0_fungi", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species"}}} \ No newline at end of file |
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| diff -r 3a4ee8bf012a -r 51b90d282704 test-data/PR24.11.1_json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/PR24.11.1_json Fri May 10 11:52:03 2019 -0400 |
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| @@ -0,0 +1,1 @@ +{"data_tables": {"dada2_taxonomy": {"path": "PR2_4.11.1.taxonomy", "name": "Protist Ribosomal Reference database (PR2) 4.11.1", "value": "PR2_4.11.1", "taxlevels": "Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species"}}} \ No newline at end of file |
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| diff -r 3a4ee8bf012a -r 51b90d282704 test-data/RefSeq_RDP2018_json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/RefSeq_RDP2018_json Fri May 10 11:52:03 2019 -0400 |
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| @@ -0,0 +1,1 @@ +{"data_tables": {"dada2_taxonomy": {"path": "RefSeq_RDP_2018_05.taxonomy", "name": "NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018)", "value": "RefSeq_RDP_2018_05", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species"}}} \ No newline at end of file |
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| diff -r 3a4ee8bf012a -r 51b90d282704 test-data/dada2_species.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dada2_species.loc Fri May 10 11:52:03 2019 -0400 |
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| @@ -0,0 +1,13 @@ +# This is a sample file distributed with Galaxy that is used to define a +# list of dada2 reference data sets for species assignment, using three +# tab separated columns: +# +# <unique_build_id> <display_name> <fasta_file_path> +# +# 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 |
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| diff -r 3a4ee8bf012a -r 51b90d282704 test-data/dada2_taxonomy.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dada2_taxonomy.loc Fri May 10 11:52:03 2019 -0400 |
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| @@ -0,0 +1,20 @@ +# This is a sample file distributed with Galaxy that is used to define a +# list of dada2 reference data sets for taxonomy assignment, using three +# tab separated columns: +# +# <unique_build_id> <display_name> <fasta_file_path> <taxlevels> +# +# 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 |
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| diff -r 3a4ee8bf012a -r 51b90d282704 test-data/greengenes13.84_json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/greengenes13.84_json Fri May 10 11:52:03 2019 -0400 |
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| @@ -0,0 +1,1 @@ +{"data_tables": {"dada2_taxonomy": {"path": "greengenes_13.84.taxonomy", "name": "GreenGenes version 13.84", "value": "greengenes_13.84", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species"}}} \ No newline at end of file |
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| diff -r 3a4ee8bf012a -r 51b90d282704 test-data/gtdb2018_json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gtdb2018_json Fri May 10 11:52:03 2019 -0400 |
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| @@ -0,0 +1,1 @@ +{"data_tables": {"dada2_taxonomy": {"path": "gtdb_2018_11.taxonomy", "name": "GTDB: Genome Taxonomy Database (Bacteria & Archaea) (11/2018)", "value": "gtdb_2018_11", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species"}}} \ No newline at end of file |
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| diff -r 3a4ee8bf012a -r 51b90d282704 test-data/hitdb1_json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hitdb1_json Fri May 10 11:52:03 2019 -0400 |
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| @@ -0,0 +1,1 @@ +{"data_tables": {"dada2_taxonomy": {"path": "hitdb_1.taxonomy", "name": "HitDB version 1 (Human InTestinal 16S rRNA)", "value": "hitdb_1", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species"}}} \ No newline at end of file |
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| diff -r 3a4ee8bf012a -r 51b90d282704 test-data/rdp16_json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rdp16_json Fri May 10 11:52:03 2019 -0400 |
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| @@ -0,0 +1,1 @@ +{"data_tables": {"dada2_species": {"path": "rdp_16.species", "name": "RDP trainset 16", "value": "rdp_16"}, "dada2_taxonomy": {"path": "rdp_16.taxonomy", "name": "RDP trainset 16", "value": "rdp_16", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species"}}} \ No newline at end of file |
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| diff -r 3a4ee8bf012a -r 51b90d282704 test-data/silva132_json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/silva132_json Fri May 10 11:52:03 2019 -0400 |
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| @@ -0,0 +1,1 @@ +{"data_tables": {"dada2_species": {"path": "silva_132.species", "name": "Silva version 132", "value": "silva_132"}, "dada2_taxonomy": {"path": "silva_132.taxonomy", "name": "Silva version 132", "value": "silva_132", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species"}}} \ No newline at end of file |
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| diff -r 3a4ee8bf012a -r 51b90d282704 test-data/silvaeuk132_json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/silvaeuk132_json Fri May 10 11:52:03 2019 -0400 |
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| @@ -0,0 +1,1 @@ +{"data_tables": {"dada2_taxonomy": {"path": "silva_euk_18S_132.taxonomy", "name": "Silva version 132 Eukaryotic 18S", "value": "silva_euk_18S_132", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species"}}} \ No newline at end of file |
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| diff -r 3a4ee8bf012a -r 51b90d282704 test-data/unite8fungi_json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/unite8fungi_json Fri May 10 11:52:03 2019 -0400 |
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| @@ -0,0 +1,1 @@ +{"data_tables": {"dada2_taxonomy": {"path": "unite_8.0_fungi.taxonomy", "name": "UNITE: General Fasta release 8.0 for Fungi", "value": "unite_8.0_fungi", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species"}}} \ No newline at end of file |
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| diff -r 3a4ee8bf012a -r 51b90d282704 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri May 10 11:52:03 2019 -0400 |
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| @@ -0,0 +1,11 @@ +<?xml version="1.0"?> +<tables> + <table name="dada2_species" comment_char="#"> + <columns>value, name, path</columns> + <file path="${__HERE__}/test-data/dada2_species.loc" /> + </table> + <table name="dada2_taxonomy" comment_char="#"> + <columns>value, name, path, taxlevels</columns> + <file path="${__HERE__}/test-data/dada2_taxonomy.loc" /> + </table> +</tables> |