Mercurial > repos > nate > data_manager_build_kraken2_database
annotate data_manager/kraken2_build_database.xml @ 0:c13785ca6192 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
author | nate |
---|---|
date | Wed, 06 Nov 2024 20:00:39 +0000 |
parents | |
children |
rev | line source |
---|---|
0
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
1 <?xml version="1.0"?> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
2 <tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
3 <description>database builder</description> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
4 <macros> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
5 <token name="@TOOL_VERSION@">2.1.3</token> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
6 <token name="@VERSION_SUFFIX@">3</token> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
7 <token name="@PROFILE@">22.01</token> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
8 <xml name="common_params"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
9 <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" /> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
10 <param name="minimizer_len" type="integer" value="31" label="Minimizer length" /> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
11 <param name="minimizer_spaces" type="integer" value="7" label="Minimizer spaces" /> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
12 <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" /> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
13 <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" /> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
14 </xml> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
15 <xml name="viral"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
16 <option value="viral">Viral (viral; ~0.5 GB)</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
17 </xml> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
18 <xml name="minusb"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
19 <option value="minusb">MinusB (archaea, viral, plasmid, human, UniVec_Core; ~8 GB)</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
20 </xml> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
21 <xml name="standard"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
22 <option value="standard">Standard-Full (archaea, bacteria, viral, plasmid, human, UniVec_Core; ~50 GB)</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
23 </xml> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
24 <xml name="standard_08gb"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
25 <option value="standard_08gb">Standard-8 (Standard with DB capped at 8 GB)</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
26 </xml> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
27 <xml name="standard_16gb"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
28 <option value="standard_16gb">Standard-16 (Standard with DB capped at 16 GB)</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
29 </xml> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
30 <xml name="pluspf"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
31 <option value="pluspf">PlusPF (Standard plus protozoa and fungi; ~50 GB)</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
32 </xml> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
33 <xml name="pluspf_08gb"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
34 <option value="pluspf_08gb">PlusPF-8 (PlusPF with DB capped at 8 GB; ~7.5 GB)</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
35 </xml> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
36 <xml name="pluspf_16gb"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
37 <option value="pluspf_16gb">PlusPF-16 (PlusPF with DB capped at 16 GB; ~15 GB)</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
38 </xml> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
39 <xml name="pluspfp"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
40 <option value="pluspfp">PlusPFP (Standard plus protozoa, fungi and plant; ~129 GB)</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
41 </xml> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
42 <xml name="pluspfp_08gb"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
43 <option value="pluspfp_08gb">PlusPFP-8 (PlusPFP with DB capped at 8 GB; ~7.5 GB)</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
44 </xml> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
45 <xml name="pluspfp_16gb"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
46 <option value="pluspfp_16gb">PlusPFP-16 (PlusPFP with DB capped at 16 GB; ~15 GB)</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
47 </xml> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
48 </macros> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
49 <xrefs> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
50 <xref type="bio.tools">kraken2</xref> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
51 </xrefs> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
52 <requirements> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
53 <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
54 <requirement type="package" version="3.13">python</requirement> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
55 </requirements> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
56 <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
57 <command detect_errors="exit_code"><![CDATA[ |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
58 python '$__tool_directory__/kraken2_build_database.py' |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
59 '$out_file' |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
60 --database-type '$database_type.database_type' |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
61 #if $database_type.database_type == "standard_local_build" |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
62 --threads \${GALAXY_SLOTS:-1} |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
63 --kmer-len $database_type.kmer_len |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
64 --minimizer-len $database_type.minimizer_len |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
65 --minimizer-spaces $database_type.minimizer_spaces |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
66 --load-factor $database_type.load_factor |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
67 $database_type.clean |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
68 #else if $database_type.database_type == "standard_prebuilt" |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
69 --prebuilt-db '$database_type.prebuild.prebuilt_db' |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
70 --prebuilt-date '$database_type.prebuild.prebuilt_date' |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
71 #else if $database_type.database_type == "minikraken" |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
72 --minikraken2-version '$database_type.minikraken2_version' |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
73 #else if $database_type.database_type == "special_prebuilt" |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
74 --prebuilt-db '$database_type.special_prebuild.prebuilt_db' |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
75 --prebuilt-date '$database_type.special_prebuild.prebuilt_date' |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
76 #else if $database_type.database_type == "special" |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
77 --threads \${GALAXY_SLOTS:-1} |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
78 --special-database-type '$database_type.special_database_type' |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
79 --kmer-len $database_type.kmer_len |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
80 --minimizer-len $database_type.minimizer_len |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
81 --minimizer-spaces $database_type.minimizer_spaces |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
82 --load-factor $database_type.load_factor |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
83 $database_type.clean |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
84 #else if $database_type.database_type == "custom" |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
85 --threads \${GALAXY_SLOTS:-1} |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
86 --custom-fasta '$database_type.custom_fasta' |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
87 --custom-database-name '$database_type.custom_database_name' |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
88 --custom-source-info '$database_type.custom_source_info' |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
89 $database_type.skip_maps |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
90 --kmer-len $database_type.kmer_len |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
91 --minimizer-len $database_type.minimizer_len |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
92 --minimizer-spaces $database_type.minimizer_spaces |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
93 --load-factor $database_type.load_factor |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
94 $database_type.clean |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
95 #end if |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
96 ]]> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
97 </command> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
98 <inputs> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
99 <conditional name="database_type"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
100 <param name="database_type" type="select" multiple="false" label="Database Type"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
101 <option value="standard_local_build">Standard, Local Build</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
102 <option value="standard_prebuilt">Pre-Built Refseq indexes</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
103 <option value="minikraken">MiniKraken</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
104 <option value="special_prebuilt">Special Pre-Built indexes</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
105 <option value="special">Special</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
106 <option value="custom">Custom</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
107 </param> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
108 <when value="standard_local_build"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
109 <expand macro="common_params" /> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
110 </when> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
111 <when value="standard_prebuilt"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
112 <conditional name="prebuild"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
113 <param name="prebuilt_date" type="select" label="Select index build date"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
114 <option value="2024-06-05">June 5, 2024</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
115 <option value="2024-01-12">January 12, 2024</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
116 <option value="2023-06-05">June 5, 2023</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
117 <option value="2022-06-07">June 7, 2022</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
118 <option value="2021-05-17">May 17, 2021</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
119 <option value="2021-01-27">January 27, 2021</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
120 <option value="2020-12-02">December 2, 2020</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
121 <option value="2020-09-19">September 19, 2020</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
122 </param> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
123 <when value="2024-06-05"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
124 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
125 <expand macro="viral"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
126 <expand macro="minusb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
127 <expand macro="standard"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
128 <expand macro="standard_08gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
129 <expand macro="standard_16gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
130 <expand macro="pluspf"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
131 <expand macro="pluspf_08gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
132 <expand macro="pluspf_16gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
133 <expand macro="pluspfp"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
134 <expand macro="pluspfp_08gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
135 <expand macro="pluspfp_16gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
136 </param> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
137 </when> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
138 <when value="2024-01-12"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
139 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
140 <expand macro="viral"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
141 <expand macro="minusb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
142 <expand macro="standard"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
143 <expand macro="standard_08gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
144 <expand macro="standard_16gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
145 <expand macro="pluspf"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
146 <expand macro="pluspf_08gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
147 <expand macro="pluspf_16gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
148 <expand macro="pluspfp"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
149 <expand macro="pluspfp_08gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
150 <expand macro="pluspfp_16gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
151 </param> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
152 </when> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
153 <when value="2023-06-05"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
154 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
155 <expand macro="viral"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
156 <expand macro="minusb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
157 <expand macro="standard"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
158 <expand macro="standard_08gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
159 <expand macro="standard_16gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
160 <expand macro="pluspf"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
161 <expand macro="pluspf_08gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
162 <expand macro="pluspf_16gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
163 <expand macro="pluspfp"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
164 <expand macro="pluspfp_08gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
165 <expand macro="pluspfp_16gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
166 </param> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
167 </when> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
168 <when value="2022-06-07"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
169 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
170 <expand macro="viral"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
171 <expand macro="minusb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
172 <expand macro="standard"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
173 <expand macro="standard_08gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
174 <expand macro="standard_16gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
175 <expand macro="pluspf"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
176 <expand macro="pluspf_08gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
177 <expand macro="pluspf_16gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
178 <expand macro="pluspfp"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
179 <expand macro="pluspfp_08gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
180 <expand macro="pluspfp_16gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
181 </param> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
182 </when> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
183 <when value="2021-05-17"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
184 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
185 <expand macro="viral"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
186 <expand macro="minusb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
187 <expand macro="standard"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
188 <expand macro="standard_08gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
189 <expand macro="standard_16gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
190 <expand macro="pluspf"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
191 <expand macro="pluspf_08gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
192 <expand macro="pluspf_16gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
193 <expand macro="pluspfp_08gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
194 <expand macro="pluspfp_16gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
195 </param> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
196 </when> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
197 <when value="2021-01-27"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
198 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
199 <expand macro="pluspf"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
200 <expand macro="pluspf_08gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
201 <expand macro="pluspf_16gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
202 <expand macro="pluspfp_08gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
203 <expand macro="pluspfp_16gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
204 </param> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
205 </when> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
206 <when value="2020-12-02"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
207 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
208 <expand macro="viral"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
209 <expand macro="minusb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
210 <expand macro="standard"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
211 <expand macro="standard_08gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
212 <expand macro="standard_16gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
213 </param> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
214 </when> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
215 <when value="2020-09-19"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
216 <param name="prebuilt_db" type="select" multiple="false" label="Select a prebuilt Refseq indexes to download"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
217 <expand macro="minusb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
218 <expand macro="standard"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
219 <expand macro="standard_08gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
220 <expand macro="standard_16gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
221 <expand macro="pluspf"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
222 <expand macro="pluspf_08gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
223 <expand macro="pluspf_16gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
224 <expand macro="pluspfp_08gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
225 <expand macro="pluspfp_16gb"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
226 </param> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
227 </when> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
228 </conditional> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
229 </when> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
230 <when value="special_prebuilt"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
231 <conditional name="special_prebuild"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
232 <param name="special_prebuilt_db" type="select" multiple="false" label="Select pre-built database to download"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
233 <option value="eupathdb48_20230407">EuPathDB-46 (April 7, 2023)</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
234 <option value="eupathdb48_20201113">EuPathDB-46 (November 13, 2020)</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
235 </param> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
236 <when value="eupathdb48_20230407"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
237 <param name="prebuilt_db" type="hidden" value="eupathdb48"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
238 <param name="prebuilt_date" type="hidden" value="2023-04-07"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
239 </when> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
240 <when value="eupathdb48_20201113"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
241 <param name="prebuilt_db" type="hidden" value="eupathdb48"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
242 <param name="prebuilt_date" type="hidden" value="2020-11-13"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
243 </when> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
244 </conditional> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
245 </when> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
246 <when value="minikraken"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
247 <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
248 <option value="v2">Version 2</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
249 <option value="v1">Version 1</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
250 </param> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
251 </when> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
252 <when value="special"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
253 <param name="special_database_type" type="select" multiple="false" label="Select database to build"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
254 <option value="greengenes">Greengenes</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
255 <option value="silva">Silva</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
256 <option value="rdp">RDP</option> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
257 </param> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
258 <expand macro="common_params" /> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
259 </when> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
260 <when value="custom"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
261 <param name="custom_fasta" type="data" format="fasta" multiple="False" label="Select history item" /> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
262 <param name="custom_database_name" type="text" label="Name for this database" /> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
263 <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" /> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
264 <param name="skip_maps" type="boolean" truevalue="--skip-maps" falsevalue="" label="Skip downloading accession number to taxid maps during taxonomy download." /> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
265 <expand macro="common_params" /> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
266 </when> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
267 </conditional> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
268 </inputs> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
269 <outputs> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
270 <data name="out_file" format="data_manager_json" /> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
271 </outputs> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
272 <tests> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
273 <test expect_num_outputs="1"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
274 <conditional name="database_type"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
275 <param name="database_type" value="custom" /> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
276 <param name="custom_fasta" value="adapter.fa" /> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
277 <param name="custom_database_name" value="custom_database" /> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
278 <param name="custom_source_info" value="from adapter.fa test data" /> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
279 <param name="skip_maps" value="true" /> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
280 <param name="kmer_len" value="35" /> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
281 <param name="minimizer_spaces" value="6"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
282 <param name="load_factor" value="0.7" /> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
283 <param name="clean" value="true"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
284 </conditional> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
285 <output name="out_file"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
286 <assert_contents> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
287 <has_text text="kraken2_databases"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
288 <has_text text="path"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
289 <has_text text="custom_database (from adapter.fa test data, kmer-len=35, minimizer-len=31, minimizer-spaces=6, load-factor=0.7)"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
290 </assert_contents> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
291 </output> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
292 </test> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
293 <test> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
294 <conditional name="database_type"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
295 <param name="database_type" value="standard_prebuilt" /> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
296 <conditional name="prebuild"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
297 <param name="prebuilt_date" value="2022-06-07"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
298 <param name="prebuilt_db" value="viral"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
299 </conditional> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
300 </conditional> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
301 <output name="out_file"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
302 <assert_contents> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
303 <has_text text="kraken2_databases"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
304 <has_text text="path"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
305 <has_text text="Viral"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
306 <has_text text="_standard_prebuilt_viral_2022-06-07"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
307 <has_text text="Version"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
308 <has_text text="Downloaded"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
309 </assert_contents> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
310 </output> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
311 </test> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
312 <!-- test with latest version --> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
313 <test> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
314 <conditional name="database_type"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
315 <param name="database_type" value="standard_prebuilt" /> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
316 <conditional name="prebuild"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
317 <param name="prebuilt_date" value="2024-01-12"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
318 <param name="prebuilt_db" value="viral"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
319 </conditional> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
320 </conditional> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
321 <output name="out_file"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
322 <assert_contents> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
323 <has_text text="kraken2_databases"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
324 <has_text text="path"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
325 <has_text text="Viral"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
326 <has_text text="_standard_prebuilt_viral_2024-01-12"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
327 <has_text text="Version"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
328 <has_text text="Downloaded"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
329 </assert_contents> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
330 </output> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
331 </test> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
332 <!-- test with first 2024 version --> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
333 <test> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
334 <conditional name="database_type"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
335 <param name="database_type" value="standard_prebuilt" /> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
336 <conditional name="prebuild"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
337 <param name="prebuilt_date" value="2024-06-05"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
338 <param name="prebuilt_db" value="viral"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
339 </conditional> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
340 </conditional> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
341 <output name="out_file"> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
342 <assert_contents> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
343 <has_text text="kraken2_databases"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
344 <has_text text="path"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
345 <has_text text="Viral"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
346 <has_text text="_standard_prebuilt_viral_2024-06-05"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
347 <has_text text="Version"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
348 <has_text text="Downloaded"/> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
349 </assert_contents> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
350 </output> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
351 </test> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
352 </tests> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
353 <help><![CDATA[ |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
354 Build Kraken2 databases or download `prebuilt Kraken2 RefSeq indexes <https://benlangmead.github.io/aws-indexes/k2>`__ |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
355 ]]></help> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
356 <citations> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
357 <citation type="doi">10.1186/s13059-019-1891-0</citation> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
358 </citations> |
c13785ca6192
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a
nate
parents:
diff
changeset
|
359 </tool> |