Mercurial > repos > dfornika > data_manager_build_kraken2_database

changeset 33:eb123ede1812 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5629d9d7d9836d32b1e501277e213ef213de3e76-dirty
author dfornika
date Tue, 30 Apr 2019 15:04:10 -0400
parents 23c68bbf573d
children 8d8ebf8367c8
files data_manager/kraken2_build_database.xml
diffstat 1 files changed, 18 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/kraken2_build_database.xml	Tue Apr 30 14:30:24 2019 -0400
+++ b/data_manager/kraken2_build_database.xml	Tue Apr 30 15:04:10 2019 -0400
@@ -1,5 +1,12 @@
 <?xml version="1.0"?>
 <tool id="kraken2_build_database" name="Kraken2 Database Builder" tool_type="manage_data" version="2.0.7_beta">
+    <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" />
+        </xml>
+    </macros>
     <description>database builder</description>
     <requirements>
         <requirement type="package" version="2.0.7_beta">kraken2</requirement>
@@ -19,10 +26,18 @@
         <conditional name="database_type">
             <param name="database_type" type="select" multiple="false" label="Database Type">
                 <option value="standard">Standard</option>
+                <option value="minikraken">MiniKraken</option>
                 <option value="special">Special</option>
                 <option value="custom">Custom</option>
             </param>
             <when value="standard">
+                <expand macro="common_params" />
+            </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="v1">Version 1</option>
+                </param>
             </when>
             <when value="special">
                 <param name="db_type" type="select" multiple="false" label="Select database to build">
@@ -30,14 +45,14 @@
                     <option value="silva">Silva</option>
                     <option value="rdp">RDP</option>
                 </param>
+                <expand macro="common_params" />
             </when>
             <when value="custom">
                 <param name="input_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" />
                 <param name="database_name" type="text" label="Name for this database" />
+                <expand macro="common_params" />
             </when>
-            <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" />
+            
         </conditional>
     </inputs>
     <outputs>