Mercurial > repos > iuc > data_manager_build_kraken2_database

annotate data_manager/kraken2_build_database.xml @ 13:150ea60a4ebc draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
author iuc
date Wed, 05 Nov 2025 13:31:52 +0000
parents bf7f964a12b7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
1 <tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
8
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
2 <description>database builder</description>
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
3 <macros>
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
4 <token name="@TOOL_VERSION@">2.1.6</token>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
5 <token name="@VERSION_SUFFIX@">0</token>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
6 <token name="@PROFILE@">24.0</token>
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
7 <xml name="common_params">
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
8 <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" />
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
9 <param name="minimizer_len" type="integer" value="31" label="Minimizer length" />
9
ba981d05e216 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 9835da32741d05d129a1a44835f66e32713770ad
iuc
parents: 8
diff changeset
10 <param name="minimizer_spaces" type="integer" value="7" label="Minimizer spaces" />
4
5f4b0a3cb38b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e"
iuc
parents: 2
diff changeset
11 <param name="load_factor" type="float" value="0.7" min="0" max="1" label="Load factor" help="Proportion of the hash table to be populated" />
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
12 <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="false" label="Clean up extra files. Note: If the extra files are removed this DB cannot be used to build a bracken DB!" />
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
13 </xml>
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
14 <xml name="viral">
8
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
15 <option value="viral">Viral (viral; ~0.5 GB)</option>
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
16 </xml>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
17 <xml name="minusb">
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
18 <option value="minusb">MinusB (archaea, viral, plasmid, human, UniVec_Core; ~8 GB)</option>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
19 </xml>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
20 <xml name="standard">
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
21 <option value="standard">Standard-Full (archaea, bacteria, viral, plasmid, human, UniVec_Core; ~50 GB)</option>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
22 </xml>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
23 <xml name="standard_08gb">
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
24 <option value="standard_08gb">Standard-8 (Standard with DB capped at 8 GB)</option>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
25 </xml>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
26 <xml name="standard_16gb">
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
27 <option value="standard_16gb">Standard-16 (Standard with DB capped at 16 GB)</option>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
28 </xml>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
29 <xml name="pluspf">
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
30 <option value="pluspf">PlusPF (Standard plus protozoa and fungi; ~50 GB)</option>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
31 </xml>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
32 <xml name="pluspf_08gb">
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
33 <option value="pluspf_08gb">PlusPF-8 (PlusPF with DB capped at 8 GB; ~7.5 GB)</option>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
34 </xml>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
35 <xml name="pluspf_16gb">
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
36 <option value="pluspf_16gb">PlusPF-16 (PlusPF with DB capped at 16 GB; ~15 GB)</option>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
37 </xml>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
38 <xml name="pluspfp">
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
39 <option value="pluspfp">PlusPFP (Standard plus protozoa, fungi and plant; ~129 GB)</option>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
40 </xml>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
41 <xml name="pluspfp_08gb">
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
42 <option value="pluspfp_08gb">PlusPFP-8 (PlusPFP with DB capped at 8 GB; ~7.5 GB)</option>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
43 </xml>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
44 <xml name="pluspfp_16gb">
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
45 <option value="pluspfp_16gb">PlusPFP-16 (PlusPFP with DB capped at 16 GB; ~15 GB)</option>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
46 </xml>
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
47 </macros>
9
ba981d05e216 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 9835da32741d05d129a1a44835f66e32713770ad
iuc
parents: 8
diff changeset
48 <xrefs>
ba981d05e216 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 9835da32741d05d129a1a44835f66e32713770ad
iuc
parents: 8
diff changeset
49 <xref type="bio.tools">kraken2</xref>
ba981d05e216 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 9835da32741d05d129a1a44835f66e32713770ad
iuc
parents: 8
diff changeset
50 </xrefs>
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
51 <requirements>
4
5f4b0a3cb38b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e"
iuc
parents: 2
diff changeset
52 <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
53 </requirements>
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
54 <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
55 <command detect_errors="exit_code"><![CDATA[
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
56 #import datetime
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
57 #import re
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
58
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
59 #set now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
60 #set commands = []
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
61 mkdir '$out_file.extra_files_path' &&
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
62
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
63 #if $database_type.database_type == "standard_prebuilt" or $database_type.database_type == "special_prebuilt" or $database_type.database_type == "amplicon_prebuilt"
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
64 #set prebuilt_name = {
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
65 'viral': "Viral",
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
66 'minusb': "MinusB (archaea, viral, plasmid, human, UniVec_Core)",
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
67 'standard': "Standard-Full (archaea, bacteria, viral, plasmid, human,UniVec_Core)",
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
68 'standard_08gb': "Standard-8 (Standard with DB capped at 8 GB)",
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
69 'standard_16gb': "Standard-16 (Standard with DB capped at 16 GB)",
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
70 'pluspf': "PlusPF (Standard plus protozoa and fungi)",
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
71 'pluspf_08gb': "PlusPF-8 (PlusPF with DB capped at 8 GB)",
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
72 'pluspf_16gb': "PlusPF-16 (PlusPF with DB capped at 16 GB)",
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
73 'pluspfp': "PlusPFP (Standard plus protozoa, fungi and plant)",
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
74 'pluspfp_08gb': "PlusPFP-8 (PlusPFP with DB capped at 8 GB)",
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
75 'pluspfp_16gb': "PlusPFP-16 (PlusPFP with DB capped at 16 GB)",
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
76 }
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
77 #set special_name = {
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
78 "core_nt_20250609": "Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (July, 2025)",
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
79 "core_nt_20241228": "Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (December, 2024)",
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
80 "core_nt_20240904": "Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (September, 2024)",
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
81 "gtdb_genome_reps_20250609": "GTDB v226 (Bacterial and archaeal)",
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
82 "gtdb_genome_reps_20241109": "GTDB v220 (Bacterial and archaeal)",
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
83 "eupathdb48_20230407": "EuPathDB-46 (April 18, 2023)",
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
84 "eupathdb48_20201113": "EuPathDB-46 (November 13, 2020)"
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
85 }
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
86 #set amplicon_name = {
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
87 "16S_Greengenes13.5_20200326": "Greengenes 13.5",
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
88 "16S_RDP11.5_20200326": "RDP 11.5",
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
89 "16S_Silva132_20200326": "Silva 132",
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
90 "16S_Silva138_20200326": "Silva 138"
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
91 }
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
92
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
93 #set date_url_str = str($database_type.prebuilt.prebuilt_date).replace('-', '')
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
94 #set display_name = prebuilt_name.get(str($database_type.prebuilt.prebuilt_db))
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
95 #if not display_name
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
96 #set display_name = special_name.get(str($database_type.prebuilt.prebuilt_db)+"_"+date_url_str)
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
97 #end if
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
98 #if not display_name
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
99 #set display_name = amplicon_name.get(str($database_type.prebuilt.prebuilt_db)+"_"+date_url_str)
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
100 #end if
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
101
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
102 #set database_value = "_".join([now, "standard_prebuilt", str($database_type.prebuilt.prebuilt_db), str($database_type.prebuilt.prebuilt_date)])
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
103 #set database_name = " ".join(["Prebuilt Refseq indexes: ", display_name, "(Version: ", str($database_type.prebuilt.prebuilt_date), "- Downloaded:", now + ")"])
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
104
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
105 ## the 16S dbs have a different link and file name
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
106 ## and are stored in a subfolder
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
107 #if $database_type.database_type == "amplicon_prebuilt"
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
108 #silent commands.append("wget https://genome-idx.s3.amazonaws.com/kraken/" + str($database_type.prebuilt.prebuilt_db) + "_" + date_url_str + ".tgz")
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
109 #silent commands.append("mkdir -p '" + $out_file.extra_files_path + "/" + database_value + "'/tmp_extract")
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
110 #silent commands.append("tar -xzf " + str($database_type.prebuilt.prebuilt_db) + "_" + date_url_str + ".tgz -C '" + $out_file.extra_files_path + "/" + database_value + "'/tmp_extract")
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
111 #silent commands.append("topdir=$(find '" + $out_file.extra_files_path + "/" + database_value + "/tmp_extract' -mindepth 1 -maxdepth 1 -type d | head -n 1)")
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
112 #silent commands.append("if [ -n \"$topdir\" ]")
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
113 #silent commands.append("then")
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
114 #silent commands.append(" mv \"$topdir\"/* '" + $out_file.extra_files_path + "/" + database_value + "/'")
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
115 #silent commands.append("fi")
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
116 #silent commands.append("rm -rf '" + $out_file.extra_files_path + "/" + database_value + "/tmp_extract'")
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
117 #else
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
118 #silent commands.append("wget https://genome-idx.s3.amazonaws.com/kraken/k2_" + str($database_type.prebuilt.prebuilt_db) + "_" + date_url_str + ".tar.gz")
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
119 #silent commands.append("mkdir -p '" + $out_file.extra_files_path + "/" + database_value + "'")
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
120 #silent commands.append("tar -xzf k2_" + str($database_type.prebuilt.prebuilt_db) + "_" + date_url_str + ".tar.gz -C '" + $out_file.extra_files_path + "/" + database_value + "'")
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
121 #end if
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
122
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
123 #else if $database_type.database_type == "minikraken"
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
124 #set database_value = "_".join([now, "minikraken2", str($database_type.minikraken2_version), "8GB"])
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
125 #set database_name = " ".join(["Minikraken2", str($database_type.minikraken2_version), "(Created:", now + ")"])
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
126
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
127 #silent commands.append("wget 'https://genome-idx.s3.amazonaws.com/kraken/minikraken2_" + str($database_type.minikraken2_version) + "_8GB_201904.tgz'")
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
128 #silent commands.append("mkdir -p '" + $out_file.extra_files_path + "'/'" + database_value + "'")
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
129 #silent commands.append("tar -xzf 'minikraken2_" + str($database_type.minikraken2_version) + "_8GB_201904.tgz' -C '" + $out_file.extra_files_path + "'/'" + database_value + "'")
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
130 #else
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
131 #if $database_type.database_type == "standard_local_build"
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
132 #set database_value = "_".join([now, "standard", "kmer-len", str($database_type.kmer_len), "minimizer-len", str($database_type.minimizer_len), "minimizer-spaces", str($database_type.minimizer_spaces), "load-factor", str($database_type.load_factor)])
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
133 #set database_name = " ".join(["Standard (Local Build)", "Created:", now + ",", "kmer-len=" + str($database_type.kmer_len) + ",", "minimizer-len=" + str($database_type.minimizer_len) + ",", "minimizer-spaces=" + str($database_type.minimizer_spaces) + ",", "load-factor=" + str($database_type.load_factor) + ")"])
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
134 #else if $database_type.database_type == "special"
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
135 #set special_database_names = {"rdp": "RDP", "greengenes": "Greengenes", "silva": "Silva"}
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
136 #set database_value = "_".join([now, str($database_type.special_database_type), "kmer-len", str($database_type.kmer_len), "minimizer-len", str($database_type.minimizer_len), "minimizer-spaces", str($database_type.minimizer_spaces), "load-factor", str($database_type.load_factor)])
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
137 #set database_name = " ".join([special_database_names[str($database_type.special_database_type)], "(Created:", now + ",", "kmer-len=" + str($database_type.kmer_len) + ",", "minimizer-len=" + str($database_type.minimizer_len) + ",", "minimizer-spaces=" + str($database_type.minimizer_spaces) + ",", "load-factor=" + str($database_type.load_factor) + ")"])
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
138 #else if $database_type.database_type == "custom"
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
139 #set custom_database_name = re.sub(r'[^\w_.-]+', '_', str($database_type.custom_database_name)).strip('_')
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
140 #set database_name = " ".join([custom_database_name, "(" + str($database_type.custom_source_info) + ",", "kmer-len=" + str($database_type.kmer_len) + ",", "minimizer-len=" + str($database_type.minimizer_len) + ",", "minimizer-spaces=" + str($database_type.minimizer_spaces) + ",", "load-factor=" + str($database_type.load_factor) + ")"])
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
141 #set database_value = "_".join([now, custom_database_name, "kmer-len", str($database_type.kmer_len), "minimizer-len", str($database_type.minimizer_len), "minimizer-spaces", str($database_type.minimizer_spaces), "load-factor", str($database_type.load_factor)])
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
142 #else
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
143 >&2 echo "invalid database_type: $database_type.database_type"
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
144 #end if
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
145
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
146 #if $database_type.database_type == "custom"
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
147 #silent command = ["kraken2-build", "--threads", '"${GALAXY_SLOTS:-1}"',
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
148 "--download-taxonomy",
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
149 "--db", "'" + $out_file.extra_files_path + "'/'" + database_value + "'",
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
150 str($database_type.skip_maps)]
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
151 #silent commands.append(" ".join(command))
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
152 #silent command = ["kraken2-build", "--threads", '"${GALAXY_SLOTS:-1}"',
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
153 "--add-to-library", "'" + str($database_type.custom_fasta) + "'",
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
154 "--db", "'" + $out_file.extra_files_path + "'/'" + database_value + "'"]
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
155 #silent commands.append(" ".join(command))
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
156 #end if
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
157
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
158 #silent command = ["kraken2-build", "--threads", '"${GALAXY_SLOTS:-1}"']
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
159 #if $database_type.database_type == "standard_local_build"
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
160 #silent command.append("--standard")
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
161 #else if $database_type.database_type == "special"
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
162 #silent command.extend(["--special", str($database_type.special_database_type)])
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
163 #else if $database_type.database_type == "custom"
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
164 #silent command.append("--build")
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
165 #end if
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
166 #silent command.extend([
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
167 "--kmer-len", str($database_type.kmer_len),
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
168 "--minimizer-len", str($database_type.minimizer_len),
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
169 "--minimizer-spaces", str($database_type.minimizer_spaces),
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
170 "--load-factor", str($database_type.load_factor),
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
171 "--db", "'" + $out_file.extra_files_path + "'/'" + database_value + "'"])
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
172 #silent commands.append(" ".join(command))
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
173
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
174 #if $database_type.clean
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
175 #silent command = ["kraken2-build", "--threads", '"${GALAXY_SLOTS:-1}"',
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
176 "--clean",
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
177 "--db", "'" + $out_file.extra_files_path + "'/'" + database_value + "'"]
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
178 #silent commands.append(" ".join(command))
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
179 #end if
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
180 #end if
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
181
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
182 #for command in commands
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
183 ## In test mode the tool executes `echo COMMAND` instead of `COMMAND`
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
184 #if $run_test_command == "false"
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
185 echo
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
186 #end if
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
187 #echo command
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
188 &&
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
189 #end for
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
190
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
191 echo '{"data_tables": {"kraken2_databases": [{"value": "$database_value", "name": "$database_name", "path": "$database_value"}]}}' > '$out_file'
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
192 ]]>
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
193 </command>
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
194 <inputs>
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
195 <conditional name="database_type">
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
196 <param name="database_type" type="select" multiple="false" label="Database Type">
5
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
iuc
parents: 4
diff changeset
197 <option value="standard_local_build">Standard, Local Build</option>
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
198 <option value="standard_prebuilt">Pre-Built Refseq indexes</option>
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
199 <option value="minikraken">MiniKraken</option>
10
4726ecf3b61b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit bb6d9b53b197610c5dbbb40c8ab590761755d91a
iuc
parents: 9
diff changeset
200 <option value="special_prebuilt">Special Pre-Built indexes</option>
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
201 <option value="amplicon_prebuilt">16S Pre-Built indexes</option>
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
202 <option value="special">Special</option>
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
203 <option value="custom">Custom</option>
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
204 </param>
5
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
iuc
parents: 4
diff changeset
205 <when value="standard_local_build">
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
206 <expand macro="common_params" />
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
207 </when>
5
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
iuc
parents: 4
diff changeset
208 <when value="standard_prebuilt">
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
209 <conditional name="prebuilt">
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
210 <param name="prebuilt_date" type="select" label="Select index build date">
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
211 <option value="2025-07-14">July 14, 2025</option>
12
bf7f964a12b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit f43fe4223c7cca2dac7549c3dee7e766378588da
iuc
parents: 11
diff changeset
212 <option value="2024-12-28">December 28, 2024</option>
11
36cdd9783e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 66be7bc4e07926c3645ba87f78702f2267fad7b3
iuc
parents: 10
diff changeset
213 <option value="2024-09-04">September 4, 2024</option>
8
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
214 <option value="2024-06-05">June 5, 2024</option>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
215 <option value="2024-01-12">January 12, 2024</option>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
216 <option value="2023-06-05">June 5, 2023</option>
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
217 <option value="2022-06-07">June 7, 2022</option>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
218 <option value="2021-05-17">May 17, 2021</option>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
219 <option value="2021-01-27">January 27, 2021</option>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
220 <option value="2020-12-02">December 2, 2020</option>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
221 <option value="2020-09-19">September 19, 2020</option>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
222 </param>
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
223 <when value="2025-07-14">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
224 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
225 <expand macro="viral"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
226 <expand macro="minusb"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
227 <expand macro="standard"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
228 <expand macro="standard_08gb"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
229 <expand macro="standard_16gb"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
230 <expand macro="pluspf"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
231 <expand macro="pluspf_08gb"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
232 <expand macro="pluspf_16gb"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
233 <expand macro="pluspfp"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
234 <expand macro="pluspfp_08gb"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
235 <expand macro="pluspfp_16gb"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
236 </param>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
237 </when>
12
bf7f964a12b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit f43fe4223c7cca2dac7549c3dee7e766378588da
iuc
parents: 11
diff changeset
238 <when value="2024-12-28">
bf7f964a12b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit f43fe4223c7cca2dac7549c3dee7e766378588da
iuc
parents: 11
diff changeset
239 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
bf7f964a12b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit f43fe4223c7cca2dac7549c3dee7e766378588da
iuc
parents: 11
diff changeset
240 <expand macro="viral"/>
bf7f964a12b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit f43fe4223c7cca2dac7549c3dee7e766378588da
iuc
parents: 11
diff changeset
241 <expand macro="minusb"/>
bf7f964a12b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit f43fe4223c7cca2dac7549c3dee7e766378588da
iuc
parents: 11
diff changeset
242 <expand macro="standard"/>
bf7f964a12b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit f43fe4223c7cca2dac7549c3dee7e766378588da
iuc
parents: 11
diff changeset
243 <expand macro="standard_08gb"/>
bf7f964a12b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit f43fe4223c7cca2dac7549c3dee7e766378588da
iuc
parents: 11
diff changeset
244 <expand macro="standard_16gb"/>
bf7f964a12b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit f43fe4223c7cca2dac7549c3dee7e766378588da
iuc
parents: 11
diff changeset
245 <expand macro="pluspf"/>
bf7f964a12b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit f43fe4223c7cca2dac7549c3dee7e766378588da
iuc
parents: 11
diff changeset
246 <expand macro="pluspf_08gb"/>
bf7f964a12b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit f43fe4223c7cca2dac7549c3dee7e766378588da
iuc
parents: 11
diff changeset
247 <expand macro="pluspf_16gb"/>
bf7f964a12b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit f43fe4223c7cca2dac7549c3dee7e766378588da
iuc
parents: 11
diff changeset
248 <expand macro="pluspfp"/>
bf7f964a12b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit f43fe4223c7cca2dac7549c3dee7e766378588da
iuc
parents: 11
diff changeset
249 <expand macro="pluspfp_08gb"/>
bf7f964a12b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit f43fe4223c7cca2dac7549c3dee7e766378588da
iuc
parents: 11
diff changeset
250 <expand macro="pluspfp_16gb"/>
bf7f964a12b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit f43fe4223c7cca2dac7549c3dee7e766378588da
iuc
parents: 11
diff changeset
251 </param>
bf7f964a12b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit f43fe4223c7cca2dac7549c3dee7e766378588da
iuc
parents: 11
diff changeset
252 </when>
11
36cdd9783e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 66be7bc4e07926c3645ba87f78702f2267fad7b3
iuc
parents: 10
diff changeset
253 <when value="2024-09-04">
36cdd9783e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 66be7bc4e07926c3645ba87f78702f2267fad7b3
iuc
parents: 10
diff changeset
254 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
36cdd9783e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 66be7bc4e07926c3645ba87f78702f2267fad7b3
iuc
parents: 10
diff changeset
255 <expand macro="viral"/>
36cdd9783e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 66be7bc4e07926c3645ba87f78702f2267fad7b3
iuc
parents: 10
diff changeset
256 <expand macro="minusb"/>
36cdd9783e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 66be7bc4e07926c3645ba87f78702f2267fad7b3
iuc
parents: 10
diff changeset
257 <expand macro="standard"/>
36cdd9783e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 66be7bc4e07926c3645ba87f78702f2267fad7b3
iuc
parents: 10
diff changeset
258 <expand macro="standard_08gb"/>
36cdd9783e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 66be7bc4e07926c3645ba87f78702f2267fad7b3
iuc
parents: 10
diff changeset
259 <expand macro="standard_16gb"/>
36cdd9783e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 66be7bc4e07926c3645ba87f78702f2267fad7b3
iuc
parents: 10
diff changeset
260 <expand macro="pluspf"/>
36cdd9783e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 66be7bc4e07926c3645ba87f78702f2267fad7b3
iuc
parents: 10
diff changeset
261 <expand macro="pluspf_08gb"/>
36cdd9783e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 66be7bc4e07926c3645ba87f78702f2267fad7b3
iuc
parents: 10
diff changeset
262 <expand macro="pluspf_16gb"/>
36cdd9783e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 66be7bc4e07926c3645ba87f78702f2267fad7b3
iuc
parents: 10
diff changeset
263 <expand macro="pluspfp"/>
36cdd9783e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 66be7bc4e07926c3645ba87f78702f2267fad7b3
iuc
parents: 10
diff changeset
264 <expand macro="pluspfp_08gb"/>
36cdd9783e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 66be7bc4e07926c3645ba87f78702f2267fad7b3
iuc
parents: 10
diff changeset
265 </param>
36cdd9783e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 66be7bc4e07926c3645ba87f78702f2267fad7b3
iuc
parents: 10
diff changeset
266 </when>
8
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
267 <when value="2024-06-05">
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
268 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
269 <expand macro="viral"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
270 <expand macro="minusb"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
271 <expand macro="standard"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
272 <expand macro="standard_08gb"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
273 <expand macro="standard_16gb"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
274 <expand macro="pluspf"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
275 <expand macro="pluspf_08gb"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
276 <expand macro="pluspf_16gb"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
277 <expand macro="pluspfp"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
278 <expand macro="pluspfp_08gb"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
279 <expand macro="pluspfp_16gb"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
280 </param>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
281 </when>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
282 <when value="2024-01-12">
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
283 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
284 <expand macro="viral"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
285 <expand macro="minusb"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
286 <expand macro="standard"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
287 <expand macro="standard_08gb"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
288 <expand macro="standard_16gb"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
289 <expand macro="pluspf"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
290 <expand macro="pluspf_08gb"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
291 <expand macro="pluspf_16gb"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
292 <expand macro="pluspfp"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
293 <expand macro="pluspfp_08gb"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
294 <expand macro="pluspfp_16gb"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
295 </param>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
296 </when>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
297 <when value="2023-06-05">
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
298 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
299 <expand macro="viral"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
300 <expand macro="minusb"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
301 <expand macro="standard"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
302 <expand macro="standard_08gb"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
303 <expand macro="standard_16gb"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
304 <expand macro="pluspf"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
305 <expand macro="pluspf_08gb"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
306 <expand macro="pluspf_16gb"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
307 <expand macro="pluspfp"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
308 <expand macro="pluspfp_08gb"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
309 <expand macro="pluspfp_16gb"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
310 </param>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
311 </when>
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
312 <when value="2022-06-07">
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
313 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
314 <expand macro="viral"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
315 <expand macro="minusb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
316 <expand macro="standard"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
317 <expand macro="standard_08gb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
318 <expand macro="standard_16gb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
319 <expand macro="pluspf"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
320 <expand macro="pluspf_08gb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
321 <expand macro="pluspf_16gb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
322 <expand macro="pluspfp"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
323 <expand macro="pluspfp_08gb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
324 <expand macro="pluspfp_16gb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
325 </param>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
326 </when>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
327 <when value="2021-05-17">
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
328 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
329 <expand macro="viral"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
330 <expand macro="minusb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
331 <expand macro="standard"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
332 <expand macro="standard_08gb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
333 <expand macro="standard_16gb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
334 <expand macro="pluspf"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
335 <expand macro="pluspf_08gb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
336 <expand macro="pluspf_16gb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
337 <expand macro="pluspfp_08gb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
338 <expand macro="pluspfp_16gb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
339 </param>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
340 </when>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
341 <when value="2021-01-27">
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
342 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
343 <expand macro="pluspf"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
344 <expand macro="pluspf_08gb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
345 <expand macro="pluspf_16gb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
346 <expand macro="pluspfp_08gb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
347 <expand macro="pluspfp_16gb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
348 </param>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
349 </when>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
350 <when value="2020-12-02">
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
351 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
352 <expand macro="viral"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
353 <expand macro="minusb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
354 <expand macro="standard"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
355 <expand macro="standard_08gb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
356 <expand macro="standard_16gb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
357 </param>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
358 </when>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
359 <when value="2020-09-19">
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
360 <param name="prebuilt_db" type="select" multiple="false" label="Select a prebuilt Refseq indexes to download">
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
361 <expand macro="minusb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
362 <expand macro="standard"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
363 <expand macro="standard_08gb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
364 <expand macro="standard_16gb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
365 <expand macro="pluspf"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
366 <expand macro="pluspf_08gb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
367 <expand macro="pluspf_16gb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
368 <expand macro="pluspfp_08gb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
369 <expand macro="pluspfp_16gb"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
370 </param>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
371 </when>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
372 </conditional>
5
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
iuc
parents: 4
diff changeset
373 </when>
10
4726ecf3b61b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit bb6d9b53b197610c5dbbb40c8ab590761755d91a
iuc
parents: 9
diff changeset
374 <when value="special_prebuilt">
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
375 <conditional name="prebuilt">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
376 <param name="xyz" type="select" multiple="false" label="Select pre-built database to download">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
377 <option value="core_nt_20250609">Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (July, 2025)</option>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
378 <option value="core_nt_20241228">Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (December, 2024)</option>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
379 <option value="core_nt_20240904">Very large collection, inclusive of GenBank, RefSeq, TPA and PDB (September, 2024)</option>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
380 <option value="gtdb_genome_reps_20250609">GTDB v226 (Bacterial and archaeal; ~497 GB) (July, 2025)</option>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
381 <option value="gtdb_genome_reps_20241109">GTDB v220 (Bacterial and archaeal; ~644 GB) (December 13, 2024)</option>
11
36cdd9783e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 66be7bc4e07926c3645ba87f78702f2267fad7b3
iuc
parents: 10
diff changeset
382 <option value="eupathdb48_20230407">EuPathDB-46 (April 18, 2023)</option>
10
4726ecf3b61b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit bb6d9b53b197610c5dbbb40c8ab590761755d91a
iuc
parents: 9
diff changeset
383 <option value="eupathdb48_20201113">EuPathDB-46 (November 13, 2020)</option>
4726ecf3b61b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit bb6d9b53b197610c5dbbb40c8ab590761755d91a
iuc
parents: 9
diff changeset
384 </param>
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
385 <when value="core_nt_20250609">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
386 <param name="prebuilt_db" type="hidden" value="core_nt"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
387 <param name="prebuilt_date" type="hidden" value="20250609"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
388 </when>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
389 <when value="core_nt_20241228">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
390 <param name="prebuilt_db" type="hidden" value="core_nt"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
391 <param name="prebuilt_date" type="hidden" value="20241228"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
392 </when>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
393 <when value="core_nt_20240904">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
394 <param name="prebuilt_db" type="hidden" value="core_nt"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
395 <param name="prebuilt_date" type="hidden" value="20240904"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
396 </when>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
397 <when value="gtdb_genome_reps_20250609">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
398 <param name="prebuilt_db" type="hidden" value="gtdb_genome_reps"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
399 <param name="prebuilt_date" type="hidden" value="2025-06-09"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
400 </when>
11
36cdd9783e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 66be7bc4e07926c3645ba87f78702f2267fad7b3
iuc
parents: 10
diff changeset
401 <when value="gtdb_genome_reps_20241109">
36cdd9783e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 66be7bc4e07926c3645ba87f78702f2267fad7b3
iuc
parents: 10
diff changeset
402 <param name="prebuilt_db" type="hidden" value="gtdb_genome_reps"/>
36cdd9783e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 66be7bc4e07926c3645ba87f78702f2267fad7b3
iuc
parents: 10
diff changeset
403 <param name="prebuilt_date" type="hidden" value="2024-11-09"/>
36cdd9783e6b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 66be7bc4e07926c3645ba87f78702f2267fad7b3
iuc
parents: 10
diff changeset
404 </when>
10
4726ecf3b61b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit bb6d9b53b197610c5dbbb40c8ab590761755d91a
iuc
parents: 9
diff changeset
405 <when value="eupathdb48_20230407">
4726ecf3b61b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit bb6d9b53b197610c5dbbb40c8ab590761755d91a
iuc
parents: 9
diff changeset
406 <param name="prebuilt_db" type="hidden" value="eupathdb48"/>
4726ecf3b61b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit bb6d9b53b197610c5dbbb40c8ab590761755d91a
iuc
parents: 9
diff changeset
407 <param name="prebuilt_date" type="hidden" value="2023-04-07"/>
4726ecf3b61b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit bb6d9b53b197610c5dbbb40c8ab590761755d91a
iuc
parents: 9
diff changeset
408 </when>
4726ecf3b61b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit bb6d9b53b197610c5dbbb40c8ab590761755d91a
iuc
parents: 9
diff changeset
409 <when value="eupathdb48_20201113">
4726ecf3b61b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit bb6d9b53b197610c5dbbb40c8ab590761755d91a
iuc
parents: 9
diff changeset
410 <param name="prebuilt_db" type="hidden" value="eupathdb48"/>
4726ecf3b61b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit bb6d9b53b197610c5dbbb40c8ab590761755d91a
iuc
parents: 9
diff changeset
411 <param name="prebuilt_date" type="hidden" value="2020-11-13"/>
4726ecf3b61b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit bb6d9b53b197610c5dbbb40c8ab590761755d91a
iuc
parents: 9
diff changeset
412 </when>
4726ecf3b61b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit bb6d9b53b197610c5dbbb40c8ab590761755d91a
iuc
parents: 9
diff changeset
413 </conditional>
4726ecf3b61b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit bb6d9b53b197610c5dbbb40c8ab590761755d91a
iuc
parents: 9
diff changeset
414 </when>
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
415 <when value="amplicon_prebuilt">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
416 <conditional name="prebuilt">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
417 <param name="xyz" type="select" multiple="false" label="Select pre-built database to download">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
418 <option value="16S_Greengenes13.5_20200326">Greengenes 13.5</option>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
419 <option value="16S_RDP11.5_20200326">RDP 11.5</option>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
420 <option value="16S_Silva132_20200326">Silva 132</option>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
421 <option value="16S_Silva138_20200326">Silva 138</option>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
422 </param>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
423 <when value="16S_Greengenes13.5_20200326">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
424 <param name="prebuilt_db" type="hidden" value="16S_Greengenes13.5"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
425 <param name="prebuilt_date" type="hidden" value="20200326"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
426 </when>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
427 <when value="16S_RDP11.5_20200326">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
428 <param name="prebuilt_db" type="hidden" value="16S_RDP11.5"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
429 <param name="prebuilt_date" type="hidden" value="20200326"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
430 </when>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
431 <when value="16S_Silva132_20200326">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
432 <param name="prebuilt_db" type="hidden" value="16S_Silva132"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
433 <param name="prebuilt_date" type="hidden" value="20200326"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
434 </when>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
435 <when value="16S_Silva138_20200326">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
436 <param name="prebuilt_db" type="hidden" value="16S_Silva138"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
437 <param name="prebuilt_date" type="hidden" value="20200326"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
438 </when>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
439 </conditional>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
440 </when>
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
441 <when value="minikraken">
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
442 <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download">
1
5348b6e2823d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be
iuc
parents: 0
diff changeset
443 <option value="v2">Version 2</option>
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
444 <option value="v1">Version 1</option>
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
445 </param>
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
446 </when>
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
447 <when value="special">
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
448 <param name="special_database_type" type="select" multiple="false" label="Select database to build">
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
449 <option value="greengenes">Greengenes</option>
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
450 <option value="silva">Silva</option>
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
451 <!-- <option value="rdp">RDP</option> https://github.com/DerrickWood/kraken2/issues/736 -->
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
452 </param>
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
453 <expand macro="common_params" />
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
454 </when>
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
455 <when value="custom">
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
456 <param name="custom_fasta" type="data" format="fasta" multiple="False" label="Select history item" />
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
457 <param name="custom_database_name" type="text" label="Name for this database" />
9
ba981d05e216 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 9835da32741d05d129a1a44835f66e32713770ad
iuc
parents: 8
diff changeset
458 <param name="custom_source_info" type="text" label="Database source info" help="Concise description of how this build has been sourced. This description will be appended (in parentheses) to the user-facing name of the build. Example: https://doi.org/10.5281/zenodo.8339822, from v1 assembly_summary.txt sequences" />
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
459 <param name="skip_maps" type="boolean" truevalue="--skip-maps" falsevalue="" label="Skip downloading accession number to taxid maps during taxonomy download." />
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
460 <expand macro="common_params" />
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
461 </when>
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
462 </conditional>
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
463 <param name="run_test_command" type="hidden"/>
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
464 </inputs>
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
465 <outputs>
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
466 <data name="out_file" format="data_manager_json" />
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
467 </outputs>
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
468 <tests>
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
469 <!-- standard_local_build -->
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
470
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
471 <test expect_num_outputs="1">
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
472 <conditional name="database_type">
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
473 <param name="database_type" value="standard_local_build" />
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
474 <param name="kmer_len" value="35" />
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
475 <param name="minimizer_spaces" value="6"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
476 <param name="load_factor" value="0.7" />
8
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
477 <param name="clean" value="true"/>
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
478 </conditional>
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
479 <param name="run_test_command" value="false"/>
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
480 <output name="out_file">
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
481 <assert_contents>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
482 <has_text text="kraken2_databases"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
483 <has_text text="path"/>
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
484 <has_text text="Standard (Local Build)"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
485 <has_text text="kmer-len=35, minimizer-len=31, minimizer-spaces=6, load-factor=0.7"/>
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
486 </assert_contents>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
487 </output>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
488 </test>
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
489
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
490 <!-- standard_prebuilt -->
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
491 <test>
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
492 <conditional name="database_type">
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
493 <param name="database_type" value="standard_prebuilt" />
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
494 <conditional name="prebuilt">
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
495 <param name="prebuilt_date" value="2022-06-07"/>
8
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
496 <param name="prebuilt_db" value="viral"/>
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
497 </conditional>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
498 </conditional>
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
499 <param name="run_test_command" value="true"/>
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
500 <output name="out_file">
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
501 <assert_contents>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
502 <has_text text="kraken2_databases"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
503 <has_text text="path"/>
8
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
504 <has_text text="Viral"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
505 <has_text text="_standard_prebuilt_viral_2022-06-07"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
506 <has_text text="Version"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
507 <has_text text="Downloaded"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
508 </assert_contents>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
509 </output>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
510 </test>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
511 <!-- test with latest version -->
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
512 <test>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
513 <conditional name="database_type">
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
514 <param name="database_type" value="standard_prebuilt" />
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
515 <conditional name="prebuilt">
8
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
516 <param name="prebuilt_date" value="2024-01-12"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
517 <param name="prebuilt_db" value="viral"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
518 </conditional>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
519 </conditional>
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
520 <param name="run_test_command" value="true"/>
8
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
521 <output name="out_file">
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
522 <assert_contents>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
523 <has_text text="kraken2_databases"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
524 <has_text text="path"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
525 <has_text text="Viral"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
526 <has_text text="_standard_prebuilt_viral_2024-01-12"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
527 <has_text text="Version"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
528 <has_text text="Downloaded"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
529 </assert_contents>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
530 </output>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
531 </test>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
532 <!-- test with first 2024 version -->
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
533 <test>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
534 <conditional name="database_type">
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
535 <param name="database_type" value="standard_prebuilt" />
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
536 <conditional name="prebuilt">
8
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
537 <param name="prebuilt_date" value="2024-06-05"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
538 <param name="prebuilt_db" value="viral"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
539 </conditional>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
540 </conditional>
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
541 <param name="run_test_command" value="true"/>
8
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
542 <output name="out_file">
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
543 <assert_contents>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
544 <has_text text="kraken2_databases"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
545 <has_text text="path"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
546 <has_text text="Viral"/>
1108eae823a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
iuc
parents: 6
diff changeset
547 <has_text text="_standard_prebuilt_viral_2024-06-05"/>
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
548 <has_text text="Version"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
549 <has_text text="Downloaded"/>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
550 </assert_contents>
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
551 </output>
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
552 </test>
13
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
553
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
554 <!-- minikraken -->
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
555
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
556 <test>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
557 <conditional name="database_type">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
558 <param name="database_type" value="minikraken" />
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
559 <param name="minikraken2_version" value="v1"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
560 </conditional>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
561 <param name="run_test_command" value="false"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
562 <output name="out_file">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
563 <assert_contents>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
564 <has_text text="kraken2_databases"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
565 <has_text text="path"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
566 <has_text text="Minikraken2"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
567 <has_text text="v1"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
568 <has_text text="Created"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
569 </assert_contents>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
570 </output>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
571 </test>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
572
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
573 <!-- special_prebuilt -->
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
574
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
575 <test>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
576 <conditional name="database_type">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
577 <param name="database_type" value="special_prebuilt" />
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
578 <conditional name="prebuilt">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
579 <param name="xyz" value="eupathdb48_20201113"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
580 <param name="prebuilt_date" value="2020-11-13"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
581 <param name="prebuilt_db" value="eupathdb48"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
582 </conditional>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
583 </conditional>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
584 <param name="run_test_command" value="false"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
585 <output name="out_file">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
586 <assert_contents>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
587 <has_text text="kraken2_databases"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
588 <has_text text="path"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
589 <has_text text="Prebuilt Refseq indexes: EuPathDB-46"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
590 <has_text text="standard_prebuilt_eupathdb48_2020-11-13"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
591 <has_text text="Prebuilt Refseq indexes"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
592 <has_text text="Downloaded"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
593 </assert_contents>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
594 </output>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
595 </test>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
596
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
597 <!-- amplicon_prebuilt -->
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
598
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
599 <test>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
600 <conditional name="database_type">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
601 <param name="database_type" value="amplicon_prebuilt" />
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
602 <conditional name="prebuilt">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
603 <param name="xyz" value="16S_Greengenes13.5_20200326"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
604 <param name="prebuilt_date" value="20200326"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
605 <param name="prebuilt_db" value="16S_Greengenes13.5"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
606 </conditional>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
607 </conditional>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
608 <param name="run_test_command" value="false"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
609 <output name="out_file">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
610 <assert_contents>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
611 <has_text text="kraken2_databases"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
612 <has_text text="path"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
613 <has_text text="16S_Greengenes13.5"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
614 </assert_contents>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
615 </output>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
616 </test>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
617
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
618 <!-- special -->
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
619
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
620 <test expect_num_outputs="1">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
621 <conditional name="database_type">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
622 <param name="database_type" value="special" />
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
623 <param name="special_database_type" value="greengenes" />
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
624 <param name="kmer_len" value="35" />
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
625 <param name="minimizer_spaces" value="6"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
626 <param name="load_factor" value="0.7" />
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
627 <param name="clean" value="true"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
628 </conditional>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
629 <param name="run_test_command" value="true"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
630 <output name="out_file">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
631 <assert_contents>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
632 <has_text text="kraken2_databases"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
633 <has_text text="path"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
634 <has_text text="Greengenes"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
635 <has_text text="kmer-len=35, minimizer-len=31, minimizer-spaces=6, load-factor=0.7"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
636 </assert_contents>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
637 </output>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
638 </test>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
639 <test expect_num_outputs="1">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
640 <conditional name="database_type">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
641 <param name="database_type" value="special" />
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
642 <param name="special_database_type" value="silva" />
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
643 <param name="kmer_len" value="35" />
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
644 <param name="minimizer_spaces" value="6"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
645 <param name="load_factor" value="0.7" />
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
646 <param name="clean" value="true"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
647 </conditional>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
648 <param name="run_test_command" value="true"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
649 <output name="out_file">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
650 <assert_contents>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
651 <has_text text="kraken2_databases"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
652 <has_text text="path"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
653 <has_text text="Silva"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
654 <has_text text="kmer-len=35, minimizer-len=31, minimizer-spaces=6, load-factor=0.7"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
655 </assert_contents>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
656 </output>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
657 </test>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
658
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
659 <!-- custom -->
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
660
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
661 <test expect_num_outputs="1">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
662 <conditional name="database_type">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
663 <param name="database_type" value="custom" />
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
664 <param name="custom_fasta" value="adapter.fa" />
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
665 <param name="custom_database_name" value="custom_database" />
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
666 <param name="custom_source_info" value="from adapter.fa test data" />
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
667 <param name="skip_maps" value="true" />
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
668 <param name="kmer_len" value="35" />
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
669 <param name="minimizer_spaces" value="6"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
670 <param name="load_factor" value="0.7" />
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
671 <param name="clean" value="true"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
672 </conditional>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
673 <param name="run_test_command" value="true"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
674 <output name="out_file">
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
675 <assert_contents>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
676 <has_text text="kraken2_databases"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
677 <has_text text="path"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
678 <has_text text="custom_database (from adapter.fa test data, kmer-len=35, minimizer-len=31, minimizer-spaces=6, load-factor=0.7)"/>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
679 </assert_contents>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
680 </output>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
681 </test>
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
682
150ea60a4ebc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_build_kraken2_database commit a108f20aebc04574a8bd0a90b955064439a50852
iuc
parents: 12
diff changeset
683
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
684 </tests>
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
685 <help><![CDATA[
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
686 Build Kraken2 databases or download `prebuilt Kraken2 RefSeq indexes <https://benlangmead.github.io/aws-indexes/k2>`__
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
687 ]]></help>
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
688 <citations>
9
ba981d05e216 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 9835da32741d05d129a1a44835f66e32713770ad
iuc
parents: 8
diff changeset
689 <citation type="doi">10.1186/s13059-019-1891-0</citation>
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
690 </citations>
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
691 </tool>