Mercurial > repos > dfornika > data_manager_build_kraken2_database
diff data_manager/kraken2_build_database.xml @ 19:ffeb852407d6 draft default tip
"planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 6f21145d4103d33c227f52dc55a7d3dcf52f4f5d-dirty"
author | dfornika |
---|---|
date | Wed, 23 Oct 2019 14:21:07 -0400 |
parents | f005b6efd096 |
children |
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--- a/data_manager/kraken2_build_database.xml Fri May 24 13:39:08 2019 -0400 +++ b/data_manager/kraken2_build_database.xml Wed Oct 23 14:21:07 2019 -0400 @@ -1,10 +1,11 @@ <?xml version="1.0"?> -<tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="2.0.8_beta"> +<tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="2.0.8_beta_galaxy1"> <macros> <xml name="common_params"> <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" /> <param name="minimizer_len" type="integer" value="31" label="Minimizer length" /> <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" /> + <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" /> </xml> </macros> <description>database builder</description> @@ -24,12 +25,14 @@ --kmer-len ${database_type.kmer_len} --minimizer-len ${database_type.minimizer_len} --minimizer-spaces ${database_type.minimizer_spaces} + ${database_type.clean} #else if $database_type.database_type == "special" --threads \${GALAXY_SLOTS:-1} --special-database-type ${database_type.special_database_type} --kmer-len ${database_type.kmer_len} --minimizer-len ${database_type.minimizer_len} --minimizer-spaces ${database_type.minimizer_spaces} + ${database_type.clean} #else if $database_type.database_type == "custom" --threads \${GALAXY_SLOTS:-1} ${database_type.skip_maps} @@ -38,6 +41,7 @@ --kmer-len ${database_type.kmer_len} --minimizer-len ${database_type.minimizer_len} --minimizer-spaces ${database_type.minimizer_spaces} + ${database_type.clean} #end if ]]> </command> @@ -54,7 +58,7 @@ </when> <when value="minikraken"> <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download"> - <option value="v2">Version 2</option> + <option value="v2">Version 2</option> <option value="v1">Version 1</option> </param> </when> @@ -72,7 +76,6 @@ <param name="skip_maps" type="boolean" truevalue="--skip-maps" falsevalue="" label="Skip downloading accession number to taxid maps during taxonomy download." /> <expand macro="common_params" /> </when> - </conditional> </inputs> <outputs>