Mercurial > repos > iuc > data_manager_build_kraken2_database
comparison data_manager/kraken2_build_database.xml @ 5:2f27f3b86827 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
| author | iuc |
|---|---|
| date | Mon, 08 Nov 2021 15:40:34 +0000 |
| parents | 0eebe086fd58 |
| children | 9002633b4737 |
comparison
equal
deleted
inserted
replaced
| 4:0eebe086fd58 | 5:2f27f3b86827 |
|---|---|
| 21 python '$__tool_directory__/kraken2_build_database.py' | 21 python '$__tool_directory__/kraken2_build_database.py' |
| 22 '${out_file}' | 22 '${out_file}' |
| 23 --database-type ${database_type.database_type} | 23 --database-type ${database_type.database_type} |
| 24 #if $database_type.database_type == "minikraken" | 24 #if $database_type.database_type == "minikraken" |
| 25 --minikraken2-version ${database_type.minikraken2_version} | 25 --minikraken2-version ${database_type.minikraken2_version} |
| 26 #else if $database_type.database_type == "standard" | 26 #else if $database_type.database_type == "standard_prebuilt" |
| 27 --standard-prebuilt-size ${database_type.standard_prebuilt_size} | |
| 28 #if $database_type.prebuilt_date_custom != "" | |
| 29 --prebuilt-date ${database_type.prebuilt_date_custom} | |
| 30 #else | |
| 31 --prebuilt-date ${database_type.prebuilt_date} | |
| 32 #end if | |
| 33 #else if $database_type.database_type == "standard_local_build" | |
| 27 --threads \${GALAXY_SLOTS:-1} | 34 --threads \${GALAXY_SLOTS:-1} |
| 28 --kmer-len ${database_type.kmer_len} | 35 --kmer-len ${database_type.kmer_len} |
| 29 --minimizer-len ${database_type.minimizer_len} | 36 --minimizer-len ${database_type.minimizer_len} |
| 30 --minimizer-spaces ${database_type.minimizer_spaces} | 37 --minimizer-spaces ${database_type.minimizer_spaces} |
| 31 --load-factor ${database_type.load_factor} | 38 --load-factor ${database_type.load_factor} |
| 52 ]]> | 59 ]]> |
| 53 </command> | 60 </command> |
| 54 <inputs> | 61 <inputs> |
| 55 <conditional name="database_type"> | 62 <conditional name="database_type"> |
| 56 <param name="database_type" type="select" multiple="false" label="Database Type"> | 63 <param name="database_type" type="select" multiple="false" label="Database Type"> |
| 57 <option value="standard">Standard</option> | 64 <option value="standard_local_build">Standard, Local Build</option> |
| 65 <option value="standard_prebuilt">Standard, Pre-Built</option> | |
| 58 <option value="minikraken">MiniKraken</option> | 66 <option value="minikraken">MiniKraken</option> |
| 59 <option value="special">Special</option> | 67 <option value="special">Special</option> |
| 60 <option value="custom">Custom</option> | 68 <option value="custom">Custom</option> |
| 61 </param> | 69 </param> |
| 62 <when value="standard"> | 70 <when value="standard_local_build"> |
| 63 <expand macro="common_params" /> | 71 <expand macro="common_params" /> |
| 72 </when> | |
| 73 <when value="standard_prebuilt"> | |
| 74 <param name="standard_prebuilt_size" type="select" multiple="false" label="Select size of prebuilt database to download"> | |
| 75 <option value="full">Standard-Full (~50 GB)</option> | |
| 76 <option value="16">Standard-16 (~16 GB)</option> | |
| 77 <option value="8">Standard-8 (~8 GB)</option> | |
| 78 </param> | |
| 79 <param name="prebuilt_date" type="select" multiple="false" optional="true" label="Select database build date"> | |
| 80 <option value="2021-05-17">May 17, 2021</option> | |
| 81 <option value="2020-12-02">December 2, 2020</option> | |
| 82 </param> | |
| 83 <param name="prebuilt_date_custom" type="text" label="Custom date (YYYY-MM-DD)" help="Any text here will overwrite the selected date above." /> | |
| 64 </when> | 84 </when> |
| 65 <when value="minikraken"> | 85 <when value="minikraken"> |
| 66 <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download"> | 86 <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download"> |
| 67 <option value="v2">Version 2</option> | 87 <option value="v2">Version 2</option> |
| 68 <option value="v1">Version 1</option> | 88 <option value="v1">Version 1</option> |