diff snippy.xml @ 6:d9c204f7042c draft

planemo upload commit 321f9fa14fb9c9ab56eec84bfcc2d0c0760bee4a

--- a/snippy.xml	Mon Sep 09 09:41:12 2019 -0400
+++ b/snippy.xml	Mon Sep 23 18:34:01 2019 -0400
@@ -81,7 +81,7 @@
                 </param>
             </when>
             <when value="history">
-                <param name="ref_file" type="data" format="fasta,genbank" 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" />
+                <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>
         <conditional name="fastq_input">
@@ -169,6 +169,7 @@
     <tests>
 
         <test>            <!-- test 0 - fasta ref no snps -->
+            <!-- <param name="ref" value="reference.fasta" ftype="fasta" /> -->
             <param name="reference_source|reference_source_selector" value="history"/>
             <param name="reference_source|ref_file" value="reference.fasta" ftype="fasta"/>
             <param name="fastq_input_selector" value="paired" />
@@ -182,6 +183,7 @@
         </test>
 
         <test>            <!-- test 1 - fasta ref one snp -->
+            <!-- <param name="ref" value="reference.fasta" ftype="fasta" /> -->
             <param name="reference_source|reference_source_selector" value="history"/>
             <param name="reference_source|ref_file" value="reference.fasta" ftype="fasta"/>
             <param name="fastq_input_selector" value="paired" />
@@ -195,6 +197,7 @@
         </test>
 
         <test>            <!-- test 2 - fasta ref one snp paired_collection -->
+            <!-- <param name="ref" value="reference.fasta" ftype="fasta" /> -->
             <param name="reference_source|reference_source_selector" value="history"/>
             <param name="reference_source|ref_file" value="reference.fasta" ftype="fasta"/>
             <param name="fastq_input_selector" value="paired_collection" />
@@ -212,6 +215,7 @@
         </test>
 
         <test>            <!-- test 3 - fasta ref one snp single -->
+            <!-- <param name="ref" value="reference.fasta" ftype="fasta" /> -->
             <param name="reference_source|reference_source_selector" value="history"/>
             <param name="reference_source|ref_file" value="reference.fasta" ftype="fasta"/>
             <param name="fastq_input_selector" value="single" />