Mercurial > repos > iuc > data_manager_build_kraken2_database

diff data_manager/kraken2_build_database.xml @ 4:5f4b0a3cb38b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e"
author iuc
date Mon, 23 Nov 2020 20:48:58 +0000
parents d861448f78b9
children 0d6cdde238ba
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line diff
--- a/data_manager/kraken2_build_database.xml	Sun Nov 22 12:41:21 2020 +0000
+++ b/data_manager/kraken2_build_database.xml	Mon Nov 23 20:48:58 2020 +0000
@@ -1,16 +1,18 @@
 <?xml version="1.0"?>
-<tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="2.0.8_beta+galaxy2" profile="18.09">
+<tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@" profile="18.09">
     <macros>
+        <token name="@TOOL_VERSION@">2.1.1</token>
         <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="load_factor" type="float" value="0.7" min="0" max="1" label="Load factor" help="Proportion of the hash table to be populated" />
             <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" />
         </xml>
     </macros>
     <description>database builder</description>
     <requirements>
-        <requirement type="package" version="2.0.8_beta">kraken2</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
         <requirement type="package" version="3.7">python</requirement>
     </requirements>
     <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
@@ -26,6 +28,7 @@
             --kmer-len ${database_type.kmer_len}
             --minimizer-len ${database_type.minimizer_len}
             --minimizer-spaces ${database_type.minimizer_spaces}
+            --load-factor ${database_type.load_factor}
             ${database_type.clean}
           #else if $database_type.database_type == "special"
             --threads \${GALAXY_SLOTS:-1}
@@ -33,6 +36,7 @@
             --kmer-len ${database_type.kmer_len}
             --minimizer-len ${database_type.minimizer_len}
             --minimizer-spaces ${database_type.minimizer_spaces}
+            --load-factor ${database_type.load_factor}
             ${database_type.clean}
           #else if $database_type.database_type == "custom"
             --threads \${GALAXY_SLOTS:-1}
@@ -42,6 +46,7 @@
             --kmer-len ${database_type.kmer_len}
             --minimizer-len ${database_type.minimizer_len}
             --minimizer-spaces ${database_type.minimizer_spaces}
+            --load-factor ${database_type.load_factor}
             ${database_type.clean}
           #end if
     ]]>