Mercurial > repos > iuc > data_manager_build_bracken_database
diff data_manager/bracken_build_database.xml @ 3:3c7d2c84cb09 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
author | iuc |
---|---|
date | Mon, 08 Nov 2021 15:51:51 +0000 |
parents | 9059edc96a85 |
children | 5c8a23ccb14a |
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--- a/data_manager/bracken_build_database.xml Sun Nov 22 12:45:23 2020 +0000 +++ b/data_manager/bracken_build_database.xml Mon Nov 08 15:51:51 2021 +0000 @@ -1,9 +1,9 @@ <?xml version="1.0"?> -<tool id="bracken_build_database" name="Bracken Database Builder" tool_type="manage_data" version="2.5+galaxy0" profile="19.01"> +<tool id="bracken_build_database" name="Bracken Database Builder" tool_type="manage_data" version="2.5+galaxy1" profile="19.01"> <description>bracken database builder</description> <requirements> <requirement type="package" version="2.5">bracken</requirement> - <requirement type="package" version="2.0.8_beta">kraken2</requirement> + <requirement type="package" version="2.1.1">kraken2</requirement> </requirements> <command> <![CDATA[ @@ -11,13 +11,20 @@ #set db_dir = os.path.basename($kraken_db.fields.path) mkdir '$db_dir' && - ln -s '${kraken_db.fields.path}'/* '$db_dir/' && + ln -s '${kraken_db.fields.path}/*' '$db_dir/' && python '$__tool_directory__/bracken_build_database.py' '${out_file}' - --kraken-db '$db_dir' + --threads \${GALAXY_SLOTS:-1} - --kmer-len ${kmer_len} - --read-len ${read_len} + #if $check_prebuilt.prebuilt == "no" + --kraken-db '$db_dir' + --kmer-len ${check_prebuilt.kmer_len} + #end if + #if $check_prebuilt.prebuilt == "yes" + --kraken-db '${kraken_db.fields.path}' + --prebuilt + #end if + --read-len ${check_prebuilt.read_len} --database-name '${database_name}' ]]> </command> @@ -27,9 +34,28 @@ <validator type="no_options" message="No Kraken2 databases are available" /> </options> </param> - <param name="kmer_len" type="integer" min="8" max="256" value="35" label="K-mer length" /> - <param name="read_len" type="integer" min="8" max="1000" value="100" label="Read length" /> - <param name="database_name" type="text" label="Database Name" /> + <conditional name="check_prebuilt"> + <param name="prebuilt" type="select" label="Use Pre-built DB"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + <param name="kmer_len" type="integer" min="8" max="256" value="35" label="K-mer length" /> + <param name="read_len" type="integer" min="8" max="1000" value="100" label="Read length" /> + </when> + <when value="yes"> + <param name="read_len" type="select" label="Read length" > + <option value="50">50</option> + <option value="75">75</option> + <option value="100">100</option> + <option value="150">150</option> + <option value="200">200</option> + <option value="250">250</option> + <option value="300">300</option> + </param> + </when> + </conditional> + <param name="database_name" type="text" label="Database Name" /> </inputs> <outputs> <data name="out_file" format="data_manager_json" />