diff snippy.xml @ 1:8cdc3f9c2dc5 draft

planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/snippy commit 41c38c65041b87dd3cdf86eca13278cabd13d998-dirty

--- a/snippy.xml	Tue Jun 25 10:53:58 2019 -0400
+++ b/snippy.xml	Tue Jun 25 11:09:37 2019 -0400
@@ -10,11 +10,9 @@
 
     <command detect_errors="exit_code"><![CDATA[
 
-        #if $reference_source.reference_source_selector == 'history':
-        ln -f -s '$reference_source.ref_file' 'foo.fna' &&
-        #else:
-        ln -f -s '$reference_source.ref_file.fields.path' 'foo.fna' &&
-        #end if
+        
+        ln -f -s '$snippy_ref.fields.path' 'foo.fna' &&
+    
 
         snippy
             --outdir 'out'
@@ -65,23 +63,11 @@
     ]]></command>
 
     <inputs>
-        <conditional name="reference_source">
-            <param name="reference_source_selector" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below. If you would like to perform self-mapping select `history` here, then choose your input file as reference.">
-                <option value="cached">Use a built-in genome index</option>
-                <option value="history">Use a genome from history and build index</option>
-            </param>
-            <when value="cached">
-                <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
-                    <options from_data_table="snippy">
-                        <validator type="no_options" message="No reference genomes are available" />
-                    </options>
-                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
-                </param>
-            </when>
-            <when value="history">
-                <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference" />
-            </when>
-        </conditional>
+        <param label="Select a reference" name="snippy_ref" type="select">
+            <options from_data_table="snippy">
+                <validator message="No database is available" type="no_options" />
+            </options>
+        </param>
         <conditional name="fastq_input">
             <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
                 <option value="paired">Paired</option>