Mercurial > repos > iuc > data_manager_build_kraken2_database

diff data_manager/kraken2_build_database.xml @ 1:5348b6e2823d 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 5f6f447482ad7e127af78204ffd583c51509a0be
author iuc
date Sat, 03 Aug 2019 05:30:50 -0400
parents a7c8b9cd05da
children d861448f78b9
line wrap: on
line diff
--- a/data_manager/kraken2_build_database.xml	Thu May 30 03:02:57 2019 -0400
+++ b/data_manager/kraken2_build_database.xml	Sat Aug 03 05:30:50 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>