data_manager_mothur_toolsuite: data_manager/fetch_mothur_reference

annotate data_manager/fetch_mothur_reference_data.py @ 3:2004bb845685 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e"

author	iuc
date	Fri, 25 Jun 2021 09:36:36 +0000
parents	2ffd2cdc5089
children

rev	line source
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	1 #!/usr/bin/env python3
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	2 #
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	3 # Data manager for reference data for the 'mothur_toolsuite' Galaxy tools
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	4 import io
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	5 import json
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	6 import optparse
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	7 import os
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	8 import shutil
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	9 import sys
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	10 import tarfile
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	11 import tempfile
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	12 import urllib.error
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	13 import urllib.parse
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	14 import urllib.request
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	15 import zipfile
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	16 from functools import reduce
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	17
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	18 # When extracting files from archives, skip names that
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	19 # start with the following strings
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	20 IGNORE_PATHS = ('.', '__MACOSX/', '__')
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	21
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	22 # Map file extensions to data table names
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	23 MOTHUR_FILE_TYPES = {".map": "map",
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	24 ".fasta": "aligndb",
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	25 ".align": "aligndb",
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	26 ".pat": "lookup",
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	27 ".tax": "taxonomy"}
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	28
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	29 # Reference data URLs
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	30 MOTHUR_REFERENCE_DATA = {
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	31 # Look up data
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	32 # http://www.mothur.org/wiki/Lookup_files
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	33 "lookup_titanium": {
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	34 "GS FLX Titanium": ["https://mothur.s3.us-east-2.amazonaws.com/wiki/lookup_titanium.zip", ]
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	35 },
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	36 "lookup_gsflx": {
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	37 "GSFLX": ["https://mothur.s3.us-east-2.amazonaws.com/wiki/lookup_gsflx.zip", ]
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	38 },
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	39 "lookup_gs20": {
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	40 "GS20": ["https://mothur.s3.us-east-2.amazonaws.com/wiki/lookup_gs20.zip", ]
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	41 },
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	42 # RDP reference files
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	43 # http://www.mothur.org/wiki/RDP_reference_files
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	44 "RDP_v18": {
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	45 "16S rRNA RDP training set 18":
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	46 [
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	47 "https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset18_062020.rdp.tgz", ],
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	48 "16S rRNA PDS training set 18":
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	49 [
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	50 "https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset18_062020.pds.tgz", ],
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	51 },
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	52 "RDP_v16": {
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	53 "16S rRNA RDP training set 16":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	54 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset16_022016.rdp.tgz", ],
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	55 "16S rRNA PDS training set 16":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	56 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset16_022016.pds.tgz", ],
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	57 },
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	58 "RDP_v14": {
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	59 "16S rRNA RDP training set 14":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	60 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset14_032015.rdp.tgz", ],
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	61 "16S rRNA PDS training set 14":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	62 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset14_032015.pds.tgz", ],
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	63 },
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	64 "RDP_v10": {
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	65 "16S rRNA RDP training set 10":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	66 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset10_082014.rdp.tgz", ],
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	67 "16S rRNA PDS training set 10":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	68 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset10_082014.pds.tgz", ],
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	69 },
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	70 "RDP_v9": {
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	71 "16S rRNA RDP training set 9":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	72 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset9_032012.rdp.zip", ],
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	73 "16S rRNA PDS training set 9":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	74 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset9_032012.pds.zip", ],
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	75 },
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	76 "RDP_v7": {
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	77 "16S rRNA RDP training set 7":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	78 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset7_112011.rdp.zip", ],
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	79 "16S rRNA PDS training set 7":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	80 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/trainset7_112011.pds.zip", ],
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	81 "8S rRNA Fungi training set 7":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	82 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/fungilsu_train_v7.zip", ],
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	83 },
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	84 "RDP_v6": {
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	85 "RDP training set 6":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	86 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/rdptrainingset.zip", ],
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	87 },
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	88 # Silva reference files
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	89 # http://www.mothur.org/wiki/Silva_reference_files
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	90 "silva_release_138.1": {
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	91 "SILVA release 138.1":
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	92 [
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	93 "https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.nr_v138_1.tgz",
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	94 "https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.seed_v138_1.tgz", ],
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	95 },
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	96 "silva_release_128": {
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	97 "SILVA release 128":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	98 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.nr_v128.tgz",
2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	99 "https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.seed_v128.tgz", ],
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	100 },
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	101 "silva_release_123": {
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	102 "SILVA release 123":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	103 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.nr_v123.tgz",
2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	104 "https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.seed_v123.tgz", ],
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	105 },
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	106 "silva_release_119": {
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	107 "SILVA release 119":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	108 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.nr_v119.tgz",
2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	109 "https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.seed_v119.tgz", ],
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	110 },
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	111 "silva_release_102": {
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	112 "SILVA release 102":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	113 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.bacteria.zip",
2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	114 "https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.archaea.zip",
2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	115 "https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.eukarya.zip", ],
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	116 },
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	117 "silva_gold_bacteria": {
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	118 "SILVA gold":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	119 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.gold.bacteria.zip", ],
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	120 },
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	121 # Greengenes
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	122 # http://www.mothur.org/wiki/Greengenes-formatted_databases
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	123 "greengenes_August2013": {
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	124 "Greengenes August 2013":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	125 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/gg_13_8_99.refalign.tgz",
2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	126 "https://mothur.s3.us-east-2.amazonaws.com/wiki/gg_13_8_99.taxonomy.tgz", ],
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	127 },
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	128 "greengenes_May2013": {
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	129 "Greengenes May 2013":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	130 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/gg_13_5_99.refalign.tgz",
2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	131 "https://mothur.s3.us-east-2.amazonaws.com/wiki/gg_13_5_99.taxonomy.tgz", ],
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	132 },
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	133 "greengenes_old": {
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	134 "Greengenes pre-May 2013":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	135 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/greengenes.alignment.zip",
2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	136 "https://mothur.s3.us-east-2.amazonaws.com/wiki/greengenes.tax.tgz", ],
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	137 },
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	138 "greengenes_gold_alignment": {
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	139 "Greengenes gold alignment":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	140 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/greengenes.gold.alignment.zip", ],
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	141 },
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	142 # Secondary structure maps
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	143 # http://www.mothur.org/wiki/Secondary_structure_map
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	144 "secondary_structure_maps_silva": {
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	145 "SILVA":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	146 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/silva_ss_map.zip", ],
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	147 },
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	148 "secondary_structure_maps_greengenes": {
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	149 "Greengenes":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	150 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/gg_ss_map.zip", ],
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	151 },
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	152 # Lane masks: not used here?
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	153 "lane_masks": {
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	154 "Greengenes-compatible":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	155 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/Lane1241.gg.filter",
2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	156 "https://mothur.s3.us-east-2.amazonaws.com/wiki/lane1287.gg.filter",
2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	157 "https://mothur.s3.us-east-2.amazonaws.com/wiki/lane1349.gg.filter", ],
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	158 "SILVA-compatible":
2 2ffd2cdc5089 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309" iuc parents: 1 diff changeset	159 ["https://mothur.s3.us-east-2.amazonaws.com/wiki/lane1349.silva.filter", ]
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	160 },
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	161 }
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	162
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	163
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	164 # Utility functions for interacting with Galaxy JSON
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	165 def read_input_json(jsonfile):
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	166 """Read the JSON supplied from the data manager tool
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	167
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	168 Returns a tuple (param_dict,extra_files_path)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	169
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	170 'param_dict' is an arbitrary dictionary of parameters
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	171 input into the tool; 'extra_files_path' is the path
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	172 to a directory where output files must be put for the
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	173 receiving data manager to pick them up.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	174
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	175 NB the directory pointed to by 'extra_files_path'
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	176 doesn't exist initially, it is the job of the script
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	177 to create it if necessary.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	178
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	179 """
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	180 with open(jsonfile) as fh:
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	181 params = json.load(fh)
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	182 return (params['param_dict'],
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	183 params['output_data'][0]['extra_files_path'])
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	184
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	185
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	186 # Utility functions for creating data table dictionaries
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	187 #
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	188 # Example usage:
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	189 # >>> d = create_data_tables_dict()
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	190 # >>> add_data_table(d,'my_data')
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	191 # >>> add_data_table_entry(dict(dbkey='hg19',value='human'))
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	192 # >>> add_data_table_entry(dict(dbkey='mm9',value='mouse'))
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	193 # >>> print(json.dumps(d))
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	194 def create_data_tables_dict():
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	195 """Return a dictionary for storing data table information
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	196
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	197 Returns a dictionary that can be used with 'add_data_table'
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	198 and 'add_data_table_entry' to store information about a
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	199 data table. It can be converted to JSON to be sent back to
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	200 the data manager.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	201
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	202 """
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	203 d = {}
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	204 d['data_tables'] = {}
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	205 return d
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	206
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	207
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	208 def add_data_table(d, table):
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	209 """Add a data table to the data tables dictionary
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	210
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	211 Creates a placeholder for a data table called 'table'.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	212
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	213 """
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	214 d['data_tables'][table] = []
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	215
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	216
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	217 def add_data_table_entry(d, table, entry):
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	218 """Add an entry to a data table
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	219
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	220 Appends an entry to the data table 'table'. 'entry'
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	221 should be a dictionary where the keys are the names of
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	222 columns in the data table.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	223
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	224 Raises an exception if the named data table doesn't
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	225 exist.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	226
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	227 """
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	228 try:
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	229 d['data_tables'][table].append(entry)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	230 except KeyError:
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	231 raise Exception("add_data_table_entry: no table '%s'" % table)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	232
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	233
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	234 # Utility functions for downloading and unpacking archive files
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	235 def download_file(url, target=None, wd=None):
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	236 """Download a file from a URL
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	237
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	238 Fetches a file from the specified URL.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	239
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	240 If 'target' is specified then the file is saved to this
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	241 name; otherwise it's saved as the basename of the URL.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	242
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	243 If 'wd' is specified then it is used as the 'working
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	244 directory' where the file will be save on the local
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	245 system.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	246
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	247 Returns the name that the file is saved with.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	248
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	249 """
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	250 print(f"Downloading {url}")
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	251 if not target:
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	252 target = os.path.basename(url)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	253 if wd:
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	254 target = os.path.join(wd, target)
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	255 print(f"Saving to {target}")
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	256 with open(target, 'wb') as fh:
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	257 url_h = urllib.request.urlopen(url)
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	258 while True:
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	259 buffer = url_h.read(io.DEFAULT_BUFFER_SIZE)
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	260 if buffer == b"":
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	261 break
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	262 fh.write(buffer)
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	263 return target
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	264
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	265
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	266 def unpack_zip_archive(filen, wd=None):
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	267 """Extract files from a ZIP archive
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	268
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	269 Given a ZIP archive, extract the files it contains
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	270 and return a list of the resulting file names and
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	271 paths.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	272
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	273 'wd' specifies the working directory to extract
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	274 the files to, otherwise they are extracted to the
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	275 current working directory.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	276
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	277 Once all the files are extracted the ZIP archive
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	278 file is deleted from the file system.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	279
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	280 """
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	281 if not zipfile.is_zipfile(filen):
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	282 print(f"{filen}: not ZIP formatted file")
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	283 return [filen]
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	284 file_list = []
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	285 with zipfile.ZipFile(filen) as z:
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	286 for name in z.namelist():
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	287 if reduce(lambda x, y: x or name.startswith(y), IGNORE_PATHS, False):
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	288 print(f"Ignoring {name}")
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	289 continue
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	290 if wd:
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	291 target = os.path.join(wd, name)
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	292 else:
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	293 target = name
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	294 if name.endswith('/'):
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	295 # Make directory
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	296 print(f"Creating dir {target}")
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	297 try:
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	298 os.makedirs(target)
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	299 except OSError:
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	300 pass
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	301 else:
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	302 # Extract file
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	303 print("Extracting {target}")
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	304 try:
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	305 os.makedirs(os.path.dirname(target))
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	306 except OSError:
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	307 pass
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	308 with open(target, 'wb') as fh:
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	309 fh.write(z.read(name))
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	310 file_list.append(target)
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	311 print(f"Removing {filen}")
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	312 os.remove(filen)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	313 return file_list
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	314
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	315
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	316 def unpack_tar_archive(filen, wd=None):
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	317 """Extract files from a TAR archive
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	318
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	319 Given a TAR archive (which optionally can be
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	320 compressed with either gzip or bz2), extract the
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	321 files it contains and return a list of the
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	322 resulting file names and paths.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	323
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	324 'wd' specifies the working directory to extract
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	325 the files to, otherwise they are extracted to the
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	326 current working directory.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	327
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	328 Once all the files are extracted the TAR archive
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	329 file is deleted from the file system.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	330
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	331 """
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	332 file_list = []
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	333 if not tarfile.is_tarfile(filen):
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	334 print(f"{filen}: not TAR file")
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	335 return [filen]
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	336 with tarfile.open(filen) as t:
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	337 for name in t.getnames():
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	338 # Check for unwanted files
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	339 if reduce(lambda x, y: x or name.startswith(y), IGNORE_PATHS, False):
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	340 print(f"Ignoring {name}")
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	341 continue
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	342 # Extract file
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	343 print(f"Extracting {name}")
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	344 t.extract(name, wd)
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	345 if wd:
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	346 target = os.path.join(wd, name)
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	347 else:
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	348 target = name
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	349 file_list.append(target)
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	350 print(f"Removing {filen}")
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	351 os.remove(filen)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	352 return file_list
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	353
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	354
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	355 def unpack_archive(filen, wd=None):
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	356 """Extract files from an archive
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	357
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	358 Wrapper function that calls the appropriate
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	359 unpacking function depending on the archive
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	360 type, and returns a list of files that have
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	361 been extracted.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	362
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	363 'wd' specifies the working directory to extract
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	364 the files to, otherwise they are extracted to the
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	365 current working directory.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	366
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	367 """
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	368 print(f"Unpack {filen}")
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	369 ext = os.path.splitext(filen)[1]
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	370 print(f"Extension: {ext}")
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	371 if ext == ".zip":
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	372 return unpack_zip_archive(filen, wd=wd)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	373 elif ext == ".tgz":
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	374 return unpack_tar_archive(filen, wd=wd)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	375 else:
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	376 return [filen]
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	377
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	378
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	379 def fetch_files(urls, wd=None, files=None):
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	380 """Download and unpack files from a list of URLs
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	381
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	382 Given a list of URLs, download and unpack each
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	383 one, and return a list of the extracted files.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	384
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	385 'wd' specifies the working directory to extract
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	386 the files to, otherwise they are extracted to the
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	387 current working directory.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	388
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	389 If 'files' is given then the list of extracted
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	390 files will be appended to this list before being
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	391 returned.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	392
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	393 """
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	394 if files is None:
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	395 files = []
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	396 for url in urls:
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	397 filen = download_file(url, wd=wd)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	398 files.extend(unpack_archive(filen, wd=wd))
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	399 return files
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	400
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	401
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	402 # Utility functions specific to the Mothur reference data
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	403 def identify_type(filen):
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	404 """Return the data table name based on the file name
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	405
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	406 """
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	407 ext = os.path.splitext(filen)[1]
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	408 try:
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	409 return MOTHUR_FILE_TYPES[ext]
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	410 except KeyError:
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	411 print(f"WARNING: unknown file type for {filen}, skipping")
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	412 return None
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	413
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	414
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	415 def get_name(filen):
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	416 """Generate a descriptive name based on the file name
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	417 """
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	418 # type_ = identify_type(filen)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	419 name = os.path.splitext(os.path.basename(filen))[0]
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	420 for delim in ('.', '_'):
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	421 name = name.replace(delim, ' ')
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	422 return name
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	423
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	424
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	425 def fetch_from_mothur_website(data_tables, target_dir, datasets):
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	426 """Fetch reference data from the Mothur website
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	427
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	428 For each dataset in the list 'datasets', download (and if
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	429 necessary unpack) the related files from the Mothur website,
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	430 copy them to the data manager's target directory, and add
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	431 references to the files to the appropriate data table.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	432
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	433 The 'data_tables' dictionary should have been created using
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	434 the 'create_data_tables_dict' and 'add_data_table' functions.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	435
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	436 Arguments:
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	437 data_tables: a dictionary containing the data table info
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	438 target_dir: directory to put the downloaded files
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	439 datasets: a list of dataset names corresponding to keys in
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	440 the MOTHUR_REFERENCE_DATA dictionary
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	441 """
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	442 # Make working dir
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	443 wd = tempfile.mkdtemp(suffix=".mothur", dir=os.getcwd())
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	444 print(f"Working dir {wd}")
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	445 # Iterate over all requested reference data URLs
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	446 for dataset in datasets:
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	447 print(f"Handling dataset '{dataset}'")
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	448 for name in MOTHUR_REFERENCE_DATA[dataset]:
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	449 for f in fetch_files(MOTHUR_REFERENCE_DATA[dataset][name], wd=wd):
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	450 type_ = identify_type(f)
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	451 name_from_file = os.path.splitext(os.path.basename(f))[0]
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	452 entry_name = f"{name_from_file} ({name})"
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	453 print(f"{type_}\t\'{entry_name}'\t.../{os.path.basename(f)}")
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	454 if type_ is not None:
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	455 # Move to target dir
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	456 ref_data_file = os.path.basename(f)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	457 f1 = os.path.join(target_dir, ref_data_file)
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	458 print(f"Moving {f} to {f1}")
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	459 shutil.move(f, f1)
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	460 # Add entry to data table
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	461 table_name = f"mothur_{type_}"
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	462 add_data_table_entry(data_tables, table_name, dict(name=entry_name, value=ref_data_file))
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	463 # Remove working dir
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	464 print(f"Removing {wd}")
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	465 shutil.rmtree(wd)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	466
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	467
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	468 def files_from_filesystem_paths(paths):
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	469 """Return list of file paths from arbitrary input paths
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	470
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	471 Given a list of filesystem paths, return a list of
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	472 full paths corresponding to all files found recursively
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	473 from under those paths.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	474
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	475 """
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	476 # Collect files to add
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	477 files = []
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	478 for path in paths:
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	479 path = os.path.abspath(path)
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	480 print(f"Examining '{path}'...")
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	481 if os.path.isfile(path):
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	482 # Store full path for file
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	483 files.append(path)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	484 elif os.path.isdir(path):
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	485 # Descend into directory and collect the files
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	486 for f in os.listdir(path):
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	487 files.extend(files_from_filesystem_paths((os.path.join(path, f), )))
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	488 else:
1 9ab05c09764a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e" iuc parents: 0 diff changeset	489 print("Not a file or directory, ignored")
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	490 return files
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	491
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	492
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	493 def import_from_server(data_tables, target_dir, paths, description, link_to_data=False):
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	494 """Import reference data from filesystem paths
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	495
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	496 Creates references to the specified file(s) on the Galaxy
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	497 server in the appropriate data table (determined from the
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	498 file extension).
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	499
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	500 The 'data_tables' dictionary should have been created using
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	501 the 'create_data_tables_dict' and 'add_data_table' functions.
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	502
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	503 Arguments:
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	504 data_tables: a dictionary containing the data table info
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	505 target_dir: directory to put copy or link to the data file
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	506 paths: list of file and/or directory paths to import
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	507 description: text to associate with the files
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	508 link_to_data: boolean, if False then copy the data file
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	509 into Galaxy (default); if True then make a symlink to
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	510 the data file
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	511
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	512 """
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	513 # Collect list of files based on input paths
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	514 files = files_from_filesystem_paths(paths)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	515 # Handle each file individually
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	516 for f in files:
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	517 type_ = identify_type(f)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	518 if type_ is None:
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	519 print(f"{f}: unrecognised type, skipped")
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	520 continue
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	521 ref_data_file = os.path.basename(f)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	522 target_file = os.path.join(target_dir, ref_data_file)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	523 entry_name = "%s" % os.path.splitext(ref_data_file)[0]
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	524 if description:
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	525 entry_name += " (%s)" % description
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	526 print(f"{type_}\t\'{entry_name}'\t.../{ref_data_file}")
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	527 # Link to or copy the data
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	528 if link_to_data:
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	529 os.symlink(f, target_file)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	530 else:
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	531 shutil.copyfile(f, target_file)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	532 # Add entry to data table
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	533 table_name = f"mothur_{type_}"
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	534 add_data_table_entry(data_tables, table_name, dict(name=entry_name, value=ref_data_file))
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	535
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	536
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	537 if __name__ == "__main__":
1 9ab05c09764a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e" iuc parents: 0 diff changeset	538 print("Starting...")
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	539
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	540 # Read command line
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	541 parser = optparse.OptionParser()
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	542 parser.add_option('--source', action='store', dest='data_source')
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	543 parser.add_option('--datasets', action='store', dest='datasets', default='')
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	544 parser.add_option('--paths', action='store', dest='paths', default=[])
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	545 parser.add_option('--description', action='store', dest='description', default='')
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	546 parser.add_option('--link', action='store_true', dest='link_to_data')
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	547 options, args = parser.parse_args()
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	548 print(f"options: {options}")
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	549 print(f"args : {args}")
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	550
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	551 # Check for JSON file
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	552 if len(args) != 1:
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	553 sys.stderr.write("Need to supply JSON file name")
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	554 sys.exit(1)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	555
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	556 jsonfile = args[0]
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	557
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	558 # Read the input JSON
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	559 params, target_dir = read_input_json(jsonfile)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	560
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	561 # Make the target directory
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	562 print(f"Making {target_dir}")
0 6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	563 os.mkdir(target_dir)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	564
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	565 # Set up data tables dictionary
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	566 data_tables = create_data_tables_dict()
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	567 add_data_table(data_tables, 'mothur_lookup')
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	568 add_data_table(data_tables, 'mothur_aligndb')
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	569 add_data_table(data_tables, 'mothur_map')
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	570 add_data_table(data_tables, 'mothur_taxonomy')
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	571
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	572 # Fetch data from specified data sources
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	573 if options.data_source == 'mothur_website':
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	574 datasets = options.datasets.split(',')
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	575 fetch_from_mothur_website(data_tables, target_dir, datasets)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	576 elif options.data_source == 'filesystem_paths':
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	577 # Check description text
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	578 description = options.description.strip()
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	579 # Get list of paths (need to remove any escapes for '\n' and '\r'
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	580 # that might have been inserted by Galaxy)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	581 paths = options.paths.replace('__cn__', '\n').replace('__cr__', '\r').split()
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	582 import_from_server(data_tables, target_dir, paths, description, link_to_data=options.link_to_data)
6160cc7447fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit c1b936b54b7133106b3181df1e104986613a5bea iuc parents: diff changeset	583 # Write output JSON
1 9ab05c09764a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e" iuc parents: 0 diff changeset	584 print("Outputting JSON")
3 2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	585 with open(jsonfile, 'w') as fh:
2004bb845685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit f845716f6ac93500f143a30abef97eaba406344e" iuc parents: 2 diff changeset	586 json.dump(data_tables, fh, sort_keys=True)
1 9ab05c09764a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e" iuc parents: 0 diff changeset	587 print("Done.")

Mercurial > repos > iuc > data_manager_mothur_toolsuite

annotate data_manager/fetch_mothur_reference_data.py @ 3:2004bb845685 draft default tip