Mercurial > repos > thanhlv > data_manager_build_ariba_database

changeset 8:fb4da292b6d0 draft

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planemo upload for repository https://github.com/thanhleviet/galaxy-tools commit 98648bbb7796db528b5685d44a2a5b761c53c19b-dirty
author thanhlv
date Sun, 19 May 2019 09:09:24 -0400
parents 8a442938a61a
children 218301fbbb99
files data_manager/ariba_database_builder.xml
diffstat 1 files changed, 13 insertions(+), 13 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/ariba_database_builder.xml	Sun May 19 08:50:27 2019 -0400
+++ b/data_manager/ariba_database_builder.xml	Sun May 19 09:09:24 2019 -0400
@@ -9,9 +9,9 @@
     <command detect_errors="exit_code">
     <![CDATA[
         #if str($library.lib_type) != "fasta"
-                python '$__tool_directory__/ariba_data_base_builder.py' '${out_file}' -t $library.lib_type -d $library.db
+                python '$__tool_directory__/ariba_database_builder.py' '${out_file}' -t $library.lib_type -d $library.db
         #else
-                python '$__tool_directory__/ariba_data_base_builder.py' '${out_file}' -t $library.lib_type -d $library.db -c $library.coding -f $library.fasta
+                python '$__tool_directory__/ariba_database_builder.py' '${out_file}' -t $library.lib_type -d $library.db -c $library.coding -f $library.fasta
         #end if
     ]]>
     </command>
@@ -23,16 +23,17 @@
                 <option value="fasta">A fasta file</option>
         </param>
         <when value="curated">
-        <param name="db" type="select" multiple="false" label="Select partial library to download">
-            <option value="card">CARD</option>
-            <option value="resfinder">Resfinder</option>
-            <option value="plasmidfinder">Plasmidfinder</option>
-            <option value="megares">Megares</option>
-            <option value="argannot">Argannot</option>
-            <option value="vfdb_core">vfdb_core</option>
-            <option value="vfdb_full">vfdb_full</option>
-            <option value="virulencefinder">virulencefinder</option>
-        </param>
+            <param name="db" type="select" multiple="false" label="Select partial library to download">
+                <option value="card">CARD</option>
+                <option value="resfinder">Resfinder</option>
+                <option value="plasmidfinder">Plasmidfinder</option>
+                <option value="megares">Megares</option>
+                <option value="argannot">Argannot</option>
+                <option value="vfdb_core">vfdb_core</option>
+                <option value="vfdb_full">vfdb_full</option>
+                <option value="virulencefinder">virulencefinder</option>
+            </param>
+        </when>
         <when value="mlst">
             <param name="db" type="select" multiple="false" label="Select a species">
                 <option value="achs">Achromobacter spp.</option>
@@ -178,7 +179,6 @@
                 <option value="yers">Yersinia spp.</option>
             </param>
         </when>
-        </when>
          <when value="fasta">
             <param name="fasta" type="data" format="fasta,fasta.gz" optional="false" />
             <param name="db" type="text" label="DB name" help = "The DB name should include no space, special characters, and must be uniquely different to the name predefined in curated and mlst list" />