diff annotate_variants.xml @ 1:99dfde12ee53 draft

planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 24cc567ad105450d1c554f09a3467eff671d9864

--- a/annotate_variants.xml	Sat Nov 11 18:20:20 2017 -0500
+++ b/annotate_variants.xml	Mon Dec 18 03:41:24 2017 -0500
@@ -31,7 +31,7 @@
 	    #echo ' '.join(str($snpeff_settings.filter).split(','))
 	  #end if
 	  --ofile '$ofile'
-	  --verbose
+	  --verbose --quiet
     ]]></command>
 
     <inputs>
@@ -62,21 +62,26 @@
                 label="Name of an installed SnpEff genome"
                 help="Your input needs to exactly match the name of an installed SnpEff database.">
                     <validator type="expression" message="A SnpEff genome is required to run this tool.">value.strip()</validator>
+                    <expand macro="lex_sam_header" message="Non-ASCII characters are not valid in SnpEff genome names." />
                 </param>
             </when>
         </conditional>
         <section name="codon_tables" title="Codon Table Configuration" expanded="false">
             <param name="genome_codon_table" type="text"
             label="Genome codon table"
-            help="If this genome uses a non-standard codon table and this fact is not declared in the SnpEff config file, specify the table here. The name you provide must match exactly the name of a codon table known to SnpEff." />
+            help="If this genome uses a non-standard codon table and this fact is not declared in the SnpEff config file, specify the table here. The name you provide must match exactly the name of a codon table known to SnpEff.">
+                <expand macro="lex_sam_header" message="Non-ASCII characters are not valid in codon table names." />
+            </param>
             <repeat name="table_specs" default="0" min="0"
             title="Codon tables to use for specific contigs"
             help="Use if certain contigs in the reference genome use a distinct codon table. A typical example is a mitochondrial genome contained as a contig in the reference genome. Contig/codon table assignments declared here will take precedence over a genome codon table set above.">
                 <param name="contig" type="text" label="contig or chromosome name">
                     <validator type="expression" message="This is a required field for a contig/codon table assignment.">value.strip()</validator>
+                    <expand macro="lex_sam_header" message="Non-ASCII characters are not allowed in contig/chromosome names" />
                 </param>
                 <param name="table" type="text" label="uses codon table">
                     <validator type="expression" message="This is a required field for a contig/codon table assignment.">value.strip()</validator>
+                    <expand macro="lex_sam_header" message="Non-ASCII characters are not valid in codon table names." />
                 </param>
             </repeat>
         </section>