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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" |
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modified:
data_manager/data_manager_fetch_mothur_reference_data.xml data_manager/fetch_mothur_reference_data.py |
| b |
| diff -r aec831b54a5b -r 0e532fc0a0a6 data_manager/data_manager_fetch_mothur_reference_data.xml --- a/data_manager/data_manager_fetch_mothur_reference_data.xml Thu Nov 28 15:47:32 2019 -0500 +++ b/data_manager/data_manager_fetch_mothur_reference_data.xml Thu Sep 17 09:37:41 2020 +0000 |
| b |
| b'@@ -1,5 +1,5 @@\n <?xml version="1.0"?>\n-<tool id="data_manager_fetch_mothur_reference_data" name="Fetch Mothur toolsuite reference data" version="0.1.4" tool_type="manage_data" profile="19.05">\n+<tool id="data_manager_fetch_mothur_reference_data" name="Fetch Mothur toolsuite reference data" version="0.1.5" tool_type="manage_data" profile="19.05">\n <description>Fetch and install reference data for Mothur</description>\n <requirements>\n <requirement type="package" version="2.7">python</requirement>\n@@ -74,6 +74,223 @@\n </assert_contents>\n </output>\n </test>\n+ <test>\n+ <param name="data_source|ref_data" value="lookup_gsflx"/>\n+ <output name="out_file">\n+ <assert_contents>\n+ <has_text text="GSFLX" />\n+ <has_text text="LookUp_GSFLX.pat" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="data_source|ref_data" value="lookup_gs20"/>\n+ <output name="out_file">\n+ <assert_contents>\n+ <has_text text="GS20" />\n+ <has_text text="LookUp_GS20.pat" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="data_source|ref_data" value="RDP_v16"/>\n+ <output name="out_file">\n+ <assert_contents>\n+ <has_text text="16S rRNA RDP training set 16" />\n+ <has_text text="trainset16_022016.rdp.fasta" />\n+ <has_text text="trainset16_022016.rdp.tax" />\n+ <has_text text="trainset16_022016.pds.fasta" />\n+ <has_text text="trainset16_022016.pds.tax" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="data_source|ref_data" value="RDP_v14"/>\n+ <output name="out_file">\n+ <assert_contents>\n+ <has_text text="16S rRNA RDP training set 14" />\n+ <has_text text="trainset14_032015.rdp.fasta" />\n+ <has_text text="trainset14_032015.rdp.tax" />\n+ <has_text text="trainset14_032015.pds.fasta" />\n+ <has_text text="trainset14_032015.pds.tax" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="data_source|ref_data" value="RDP_v10"/>\n+ <output name="out_file">\n+ <assert_contents>\n+ <has_text text="16S rRNA RDP training set 10" />\n+ <has_text text="trainset10_082014.rdp.fasta" />\n+ <has_text text="trainset10_082014.rdp.tax" />\n+ <has_text text="trainset10_082014.pds.fasta" />\n+ <has_text text="trainset10_082014.pds.tax" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="data_source|ref_data" value="RDP_v9"/>\n+ <output name="out_file">\n+ <assert_contents>\n+ <has_text text="16S rRNA PDS training set 9" />\n+ <has_text text="trainset9_032012.rdp.fasta" />\n+ <has_text text="trainset9_032012.rdp.tax" />\n+ <has_text text="trainset9_032012.pds.fasta" />\n+ <has_text text="trainset9_032012.pds.tax" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="data_source|ref_data" value="RDP_v7"/>\n+ <output name="out_file">\n+ <assert_contents>\n+ <has_text text="16S rRNA RDP training set 7" />\n+ <has_text text="FungiLSU_train_1400bp_8506_mod.fasta" />\n+ <has_text text="FungiLSU_train_1400bp_8506_mod.tax" />\n+ <has_text text="trainse'..b'_file">\n+ <assert_contents>\n+ <has_text text="SILVA release 102" />\n+ <has_text text="silva.bacteria.fasta" />\n+ <has_text text="silva.gold.ng.fasta" />\n+ <has_text text="nogap.archaea.fasta" />\n+ <has_text text="silva.archaea.fasta" />\n+ <has_text text="nogap.eukarya.fasta" />\n+ <has_text text="silva.eukarya.fasta" />\n+ <has_text text="silva.bacteria.gg.tax" />\n+ <has_text text="silva.bacteria.ncbi.tax" />\n+ <has_text text="silva.bacteria.rdp.tax" />\n+ <has_text text="silva.bacteria.rdp6.tax" />\n+ <has_text text="silva.bacteria.silva.tax" />\n+ <has_text text="silva.archaea.gg.tax" />\n+ <has_text text="silva.archaea.ncbi.tax" />\n+ <has_text text="silva.archaea.rdp.tax" />\n+ <has_text text="silva.archaea.silva.tax" />\n+ <has_text text="silva.eukarya.ncbi.tax" />\n+ <has_text text="silva.eukarya.silva.tax" />\n+ </assert_contents>\n+ </output>\n+ </test>-->\n+\n+ <!-- also greengenes is large (400MB-1.5GB) so only tests for older\n+ (smaller) releases are executed -->\n+ <!--<test>\n+ <param name="data_source|ref_data" value="greengenes_August2013"/>\n+ <output name="out_file">\n+ <assert_contents>\n+ <has_text text="Greengenes August 2013" />\n+ <has_text text="gg_13_8_99.gg.tax" />\n+ <has_text text="gg_13_8_99.fasta" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="data_source|ref_data" value="greengenes_May2013"/>\n+ <output name="out_file">\n+ <assert_contents>\n+ <has_text text="Greengenes May 2013" />\n+ <has_text text="gg_13_5_99.pds.tax" />\n+ <has_text text="gg_13_5_99.gg.tax" />\n+ <has_text text="gg_13_5_99.align" />\n+ <has_text text="gg_13_5_99.fasta" />\n+ </assert_contents>\n+ </output>\n+ </test>-->\n+ <test>\n+ <param name="data_source|ref_data" value="greengenes_old"/>\n+ <output name="out_file">\n+ <assert_contents>\n+ <has_text text="Greengenes pre-May 2013" />\n+ <has_text text="gg_99.pds.tax" />\n+ <has_text text="core_set_aligned.imputed.fasta" />\n+ <has_text text="gg_99.pds.ng.fasta" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="data_source|ref_data" value="greengenes_gold_alignment"/>\n+ <output name="out_file">\n+ <assert_contents>\n+ <has_text text="Greengenes gold alignment" />\n+ <has_text text="rRNA16S.gold.NAST_ALIGNED.fasta" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+\n+ <test>\n+ <param name="data_source|ref_data" value="secondary_structure_maps_silva"/>\n+ <output name="out_file">\n+ <assert_contents>\n+ <has_text text="SILVA" />\n+ <has_text text="silva.ss.map" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="data_source|ref_data" value="secondary_structure_maps_greengenes"/>\n+ <output name="out_file">\n+ <assert_contents>\n+ <has_text text="Greengenes" />\n+ <has_text text="gg.ss.map" />\n+ </assert_contents>\n+ </output>\n+ </test>\n </tests>\n <help>\n .. class:: infomark\n' |
| b |
| diff -r aec831b54a5b -r 0e532fc0a0a6 data_manager/fetch_mothur_reference_data.py --- a/data_manager/fetch_mothur_reference_data.py Thu Nov 28 15:47:32 2019 -0500 +++ b/data_manager/fetch_mothur_reference_data.py Thu Sep 17 09:37:41 2020 +0000 |
| [ |
| b'@@ -10,6 +10,7 @@\n import tempfile\n import urllib2\n import zipfile\n+from functools import reduce\n \n # When extracting files from archives, skip names that\n # start with the following strings\n@@ -27,118 +28,118 @@\n # Look up data\n # http://www.mothur.org/wiki/Lookup_files\n "lookup_titanium": {\n- "GS FLX Titanium": ["http://www.mothur.org/w/images/9/96/LookUp_Titanium.zip", ]\n+ "GS FLX Titanium": ["https://mothur.s3.us-east-2.amazonaws.com/wiki/lookup_titanium.zip", ]\n },\n "lookup_gsflx": {\n- "GSFLX": ["http://www.mothur.org/w/images/8/84/LookUp_GSFLX.zip", ]\n+ "GSFLX": ["https://mothur.s3.us-east-2.amazonaws.com/wiki/lookup_gsflx.zip", ]\n },\n "lookup_gs20": {\n- "GS20": ["http://www.mothur.org/w/images/7/7b/LookUp_GS20.zip", ]\n+ "GS20": ["https://mothur.s3.us-east-2.amazonaws.com/wiki/lookup_gs20.zip", ]\n },\n # RDP reference files\n # http://www.mothur.org/wiki/RDP_reference_files\n "RDP_v16": {\n "16S rRNA RDP training set 16":\n- ["https://mothur.org/w/images/d/dc/Trainset16_022016.rdp.tgz", ],\n+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset16_022016.rdp.tgz", ],\n "16S rRNA PDS training set 16":\n- ["https://mothur.org/w/images/c/c3/Trainset16_022016.pds.tgz", ],\n+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset16_022016.pds.tgz", ],\n },\n "RDP_v14": {\n "16S rRNA RDP training set 14":\n- ["https://mothur.org/w/images/6/6c/Trainset14_032015.rdp.tgz", ],\n+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset14_032015.rdp.tgz", ],\n "16S rRNA PDS training set 14":\n- ["https://mothur.org/w/images/8/88/Trainset14_032015.pds.tgz", ],\n+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset14_032015.pds.tgz", ],\n },\n "RDP_v10": {\n "16S rRNA RDP training set 10":\n- ["http://www.mothur.org/w/images/b/b5/Trainset10_082014.rdp.tgz", ],\n+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset10_082014.rdp.tgz", ],\n "16S rRNA PDS training set 10":\n- ["http://www.mothur.org/w/images/2/24/Trainset10_082014.pds.tgz", ],\n+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset10_082014.pds.tgz", ],\n },\n "RDP_v9": {\n "16S rRNA RDP training set 9":\n- ["http://www.mothur.org/w/images/7/72/Trainset9_032012.rdp.zip", ],\n+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset9_032012.rdp.zip", ],\n "16S rRNA PDS training set 9":\n- ["http://www.mothur.org/w/images/5/59/Trainset9_032012.pds.zip", ],\n+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset9_032012.pds.zip", ],\n },\n "RDP_v7": {\n "16S rRNA RDP training set 7":\n- ["http://www.mothur.org/w/images/2/29/Trainset7_112011.rdp.zip", ],\n+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset7_112011.rdp.zip", ],\n "16S rRNA PDS training set 7":\n- ["http://www.mothur.org/w/images/4/4a/Trainset7_112011.pds.zip", ],\n+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset7_112011.pds.zip", ],\n "8S rRNA Fungi training set 7":\n- ["http://www.mothur.org/w/images/3/36/FungiLSU_train_v7.zip", ],\n+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/fungilsu_train_v7.zip", ],\n },\n "RDP_v6": {\n "RDP training set 6":\n- ["http://www.mothur.org/w/images/4/49/RDPTrainingSet.zip", ],\n+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/rdptrainingset.zip", ],\n },\n # Silva reference files\n # http://www.mothur.org/wiki/Silva_reference_files\n "silva_release_128": {\n "SILVA release 128":\n- ["https://mothur.org/w/images/b/b4/Silva.nr_v128.tgz",\n- "https://mothur.org/w/images/a/a4/Silva.seed_v128.tgz", ],\n+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.nr_v128.tgz",\n+ "https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.seed_v128.tgz",'..b't-2.amazonaws.com/wiki/silva.nr_v123.tgz",\n+ "https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.seed_v123.tgz", ],\n },\n "silva_release_119": {\n "SILVA release 119":\n- ["http://www.mothur.org/w/images/2/27/Silva.nr_v119.tgz",\n- "http://www.mothur.org/w/images/5/56/Silva.seed_v119.tgz", ],\n+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.nr_v119.tgz",\n+ "https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.seed_v119.tgz", ],\n },\n "silva_release_102": {\n "SILVA release 102":\n- ["http://www.mothur.org/w/images/9/98/Silva.bacteria.zip",\n- "http://www.mothur.org/w/images/3/3c/Silva.archaea.zip",\n- "http://www.mothur.org/w/images/1/1a/Silva.eukarya.zip", ],\n+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.bacteria.zip",\n+ "https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.archaea.zip",\n+ "https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.eukarya.zip", ],\n },\n "silva_gold_bacteria": {\n "SILVA gold":\n- ["http://www.mothur.org/w/images/f/f1/Silva.gold.bacteria.zip", ],\n+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.gold.bacteria.zip", ],\n },\n # Greengenes\n # http://www.mothur.org/wiki/Greengenes-formatted_databases\n "greengenes_August2013": {\n "Greengenes August 2013":\n- ["http://www.mothur.org/w/images/1/19/Gg_13_8_99.refalign.tgz",\n- "http://www.mothur.org/w/images/6/68/Gg_13_8_99.taxonomy.tgz", ],\n+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/gg_13_8_99.refalign.tgz",\n+ "https://mothur.s3.us-east-2.amazonaws.com/wiki/gg_13_8_99.taxonomy.tgz", ],\n },\n "greengenes_May2013": {\n "Greengenes May 2013":\n- ["http://www.mothur.org/w/images/c/cd/Gg_13_5_99.refalign.tgz",\n- "http://www.mothur.org/w/images/9/9d/Gg_13_5_99.taxonomy.tgz", ],\n+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/gg_13_5_99.refalign.tgz",\n+ "https://mothur.s3.us-east-2.amazonaws.com/wiki/gg_13_5_99.taxonomy.tgz", ],\n },\n "greengenes_old": {\n "Greengenes pre-May 2013":\n- ["http://www.mothur.org/w/images/7/72/Greengenes.alignment.zip",\n- "http://www.mothur.org/w/images/1/16/Greengenes.tax.tgz", ],\n+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/greengenes.alignment.zip",\n+ "https://mothur.s3.us-east-2.amazonaws.com/wiki/greengenes.tax.tgz", ],\n },\n "greengenes_gold_alignment": {\n "Greengenes gold alignment":\n- ["http://www.mothur.org/w/images/2/21/Greengenes.gold.alignment.zip", ],\n+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/greengenes.gold.alignment.zip", ],\n },\n # Secondary structure maps\n # http://www.mothur.org/wiki/Secondary_structure_map\n "secondary_structure_maps_silva": {\n "SILVA":\n- ["http://www.mothur.org/w/images/6/6d/Silva_ss_map.zip", ],\n+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/silva_ss_map.zip", ],\n },\n "secondary_structure_maps_greengenes": {\n "Greengenes":\n- ["http://www.mothur.org/w/images/4/4b/Gg_ss_map.zip", ],\n+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/gg_ss_map.zip", ],\n },\n # Lane masks: not used here?\n "lane_masks": {\n "Greengenes-compatible":\n- ["http://www.mothur.org/w/images/2/2a/Lane1241.gg.filter",\n- "http://www.mothur.org/w/images/a/a0/Lane1287.gg.filter",\n- "http://www.mothur.org/w/images/3/3d/Lane1349.gg.filter", ],\n+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/Lane1241.gg.filter",\n+ "https://mothur.s3.us-east-2.amazonaws.com/wiki/lane1287.gg.filter",\n+ "https://mothur.s3.us-east-2.amazonaws.com/wiki/lane1349.gg.filter", ],\n "SILVA-compatible":\n- ["http://www.mothur.org/w/images/6/6d/Lane1349.silva.filter", ]\n+ ["https://mothur.s3.us-east-2.amazonaws.com/wiki/lane1349.silva.filter", ]\n },\n }\n \n' |