changeset 1:8352ffae5413 draft

Deleted selected files

--- a/data_manager/ariba_database_builder.xml.bk	Tue Jan 08 11:04:25 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,41 +0,0 @@
-<?xml version="1.0"?>
-<tool id="ariba_database_builder" name="ARIBA build database" tool_type="manage_data" version="@VERSION@">
-    <description>database builder</description>
-     <expand macro="requirements" />
-    <version_command>ariba version | head head -n 1</version_command>
-    <command detect_errors="exit_code">
-    <![CDATA[
-        #set $library_list = str($libraries).split(',')
-        mkdir ariba-database && cd ariba-database &&
-        #for $library in $library_list:
-            #if str($library) != 'None':
-                ariba getref $library _tmp_db && ariba prepareref -f _tmp_db.fa -m _tmp_db.tsv $library &&
-            #end if
-        #end for
-        #for $fasta in $input_fasta:
-            #if str($fasta) != 'None':
-                ariba preparef --all_coding no $fasta $fasta    &&
-            #end if
-        #end for
-        cd .. && 
-        python '$__tool_directory__/ariba_data_base_builder.py' --db '${database_name}' --out '${out_file}'
-    ]]>
-    </command>
-    <inputs>
-        <param name="database_name" type="text" label="Name for this database" />
-        <param name="libraries" type="select" multiple="true" label="Select partial library to download">
-            <option value="card">CARD</option>
-            <option value="resfinder">Resfinder</option>
-            <option value="plasmidfinder">Plasmidfinder</option>
-        </param>
-        <param name="input_fasta" type="data" format="fasta" multiple="True" optional="true" label="Select history item" />
-    </inputs>
-    <outputs>
-        <data name="out_file" format="data_manager_json" />
-    </outputs>
-    <help>
-    </help>
-    <citations>
-        <citation type="doi">110.1099/mgen.0.000131</citation>
-    </citations>
-</tool>