Mercurial > repos > iuc > data_manager_dada2

changeset 1:bf7b2c14cabc draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit a82e4981dac025c909244acd7127c215bdb519a7"
author iuc
date Thu, 05 Dec 2019 17:58:52 -0500
parents f57c13f5878b
children a6a81f921701
files data_manager/dada2_fetcher.xml data_manager/data_manager.py test-data/PR24.11.1_json test-data/RefSeq_RDP2018_json 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 test-data/unite8fungisingletons_json
diffstat 12 files changed, 16 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/dada2_fetcher.xml	Fri Nov 08 18:47:32 2019 -0500
+++ b/data_manager/dada2_fetcher.xml	Thu Dec 05 17:58:52 2019 -0500
@@ -1,6 +1,9 @@
 <?xml version="1.0"?>
-<tool id="dada2_fetcher" name="dada2 data manager" tool_type="manage_data" version="0.0.7">
+<tool id="dada2_fetcher" name="dada2 data manager" tool_type="manage_data" profile="18.09" version="0.0.8">
     <description>Download reference databases</description>
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
     <command detect_errors="exit_code"><![CDATA[
     python '$__tool_directory__/data_manager.py'
     --out '$out_file'
--- a/data_manager/data_manager.py	Fri Nov 08 18:47:32 2019 -0500
+++ b/data_manager/data_manager.py	Thu Dec 05 17:58:52 2019 -0500
@@ -120,8 +120,8 @@
         data_manager_entry['path'] = dataset + ".species"
         data_manager_json["data_tables"]["dada2_species"] = data_manager_entry
 
-    with file(outjson, 'w') as jf:
-        jf.write(json.dumps(data_manager_json))
+    with open(outjson, 'w') as jf:
+        jf.write(json.dumps(data_manager_json, sort_keys=True))
 
 
 if __name__ == '__main__':
--- a/test-data/PR24.11.1_json	Fri Nov 08 18:47:32 2019 -0500
+++ b/test-data/PR24.11.1_json	Thu Dec 05 17:58:52 2019 -0500
@@ -1,1 +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
+{"data_tables": {"dada2_taxonomy": {"name": "Protist Ribosomal Reference database (PR2) 4.11.1", "path": "PR2_4.11.1.taxonomy", "taxlevels": "Kingdom,Supergroup,Division,Class,Order,Family,Genus,Species", "value": "PR2_4.11.1"}}}
\ No newline at end of file
--- a/test-data/RefSeq_RDP2018_json	Fri Nov 08 18:47:32 2019 -0500
+++ b/test-data/RefSeq_RDP2018_json	Thu Dec 05 17:58:52 2019 -0500
@@ -1,1 +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
+{"data_tables": {"dada2_taxonomy": {"name": "NCBI RefSeq 16S rRNA database supplemented by RDP (05/2018)", "path": "RefSeq_RDP_2018_05.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "RefSeq_RDP_2018_05"}}}
\ No newline at end of file
--- a/test-data/greengenes13.84_json	Fri Nov 08 18:47:32 2019 -0500
+++ b/test-data/greengenes13.84_json	Thu Dec 05 17:58:52 2019 -0500
@@ -1,1 +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
+{"data_tables": {"dada2_taxonomy": {"name": "GreenGenes version 13.84", "path": "greengenes_13.84.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "greengenes_13.84"}}}
\ No newline at end of file
--- a/test-data/gtdb2018_json	Fri Nov 08 18:47:32 2019 -0500
+++ b/test-data/gtdb2018_json	Thu Dec 05 17:58:52 2019 -0500
@@ -1,1 +1,1 @@
-{"data_tables": {"dada2_taxonomy": {"path": "gtdb_2018_11.taxonomy", "name": "GTDB: Genome Taxonomy Database (Bacteria &amp; Archaea) (11/2018)", "value": "gtdb_2018_11", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species"}}}
\ No newline at end of file
+{"data_tables": {"dada2_taxonomy": {"name": "GTDB: Genome Taxonomy Database (Bacteria &amp; Archaea) (11/2018)", "path": "gtdb_2018_11.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "gtdb_2018_11"}}}
\ No newline at end of file
--- a/test-data/hitdb1_json	Fri Nov 08 18:47:32 2019 -0500
+++ b/test-data/hitdb1_json	Thu Dec 05 17:58:52 2019 -0500
@@ -1,1 +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
+{"data_tables": {"dada2_taxonomy": {"name": "HitDB version 1 (Human InTestinal 16S rRNA)", "path": "hitdb_1.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "hitdb_1"}}}
\ No newline at end of file
--- a/test-data/rdp16_json	Fri Nov 08 18:47:32 2019 -0500
+++ b/test-data/rdp16_json	Thu Dec 05 17:58:52 2019 -0500
@@ -1,1 +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
+{"data_tables": {"dada2_species": {"name": "RDP trainset 16", "path": "rdp_16.species", "value": "rdp_16"}, "dada2_taxonomy": {"name": "RDP trainset 16", "path": "rdp_16.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "rdp_16"}}}
\ No newline at end of file
--- a/test-data/silva132_json	Fri Nov 08 18:47:32 2019 -0500
+++ b/test-data/silva132_json	Thu Dec 05 17:58:52 2019 -0500
@@ -1,1 +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
+{"data_tables": {"dada2_species": {"name": "Silva version 132", "path": "silva_132.species", "value": "silva_132"}, "dada2_taxonomy": {"name": "Silva version 132", "path": "silva_132.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "silva_132"}}}
\ No newline at end of file
--- a/test-data/silvaeuk132_json	Fri Nov 08 18:47:32 2019 -0500
+++ b/test-data/silvaeuk132_json	Thu Dec 05 17:58:52 2019 -0500
@@ -1,1 +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
+{"data_tables": {"dada2_taxonomy": {"name": "Silva version 132 Eukaryotic 18S", "path": "silva_euk_18S_132.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "silva_euk_18S_132"}}}
\ No newline at end of file
--- a/test-data/unite8fungi_json	Fri Nov 08 18:47:32 2019 -0500
+++ b/test-data/unite8fungi_json	Thu Dec 05 17:58:52 2019 -0500
@@ -1,1 +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
+{"data_tables": {"dada2_taxonomy": {"name": "UNITE: General Fasta release 8.0 for Fungi", "path": "unite_8.0_fungi.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "unite_8.0_fungi"}}}
\ No newline at end of file
--- a/test-data/unite8fungisingletons_json	Fri Nov 08 18:47:32 2019 -0500
+++ b/test-data/unite8fungisingletons_json	Thu Dec 05 17:58:52 2019 -0500
@@ -1,1 +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
+{"data_tables": {"dada2_taxonomy": {"name": "UNITE: General Fasta release 8.0 for Fungi including global and 97% singletons", "path": "unite_8.0_fungi_singletons.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "unite_8.0_fungi_singletons"}}}
\ No newline at end of file