# HG changeset patch
# User jpetteng
# Date 1515603022 18000
# Node ID ec569c3c11e2b64ee866f33eae34aebfc13ea451
# Parent  8ae7b0f143176989cf8857469b6559ec7ff29d31
Uploaded

diff -r 8ae7b0f14317 -r ec569c3c11e2 ectyper.xml
--- a/ectyper.xml	Tue Jan 09 16:13:32 2018 -0500
+++ b/ectyper.xml	Wed Jan 10 11:50:22 2018 -0500
@@ -12,7 +12,7 @@
         ln -s $jobtype.fastq2 sample_2.fastq;  
       #end if
 
-      python $__tool_directory__/bin/ectyper
+      python $__tool_directory__/bin/ectyper 
       #if $jobtype.select == "asm"
         -i sample.fasta
       #else if $jobtype.select == "se"
@@ -20,15 +20,9 @@
       #else if $jobtype.select == "pe"
         -i sample_1.fastq sample_2.fastq
       #end if
-
-	  #if $options.percent_identity
-	      -d  $options.percent_identity
-	  #end if
-
-	  #if $options.percent_length
-		  -l $options.percent_length
-	  #end if
-	  
+      -d  $percent_identity
+	  -l $percent_length
+  
       cat  ectyper_result*/ectyper_result.txt > results.txt; 
 
     ]]></command>
@@ -51,10 +45,8 @@
         </when>
       </conditional>
 
-      <conditional name="options">
-        <param name="percent_identity" type="integer" format="txt" label="Percent identity required for an allele match [default 90]" value="90" />
-        <param name="percent_length" type="integer" format="txt" label="Percent length required for an allele match [default 50]" value="50" />
-      </conditional>
+      <param name="percent_identity" type="integer" label="Percent identity required for an allele match [default 90]" value="90" />
+      <param name="percent_length" type="integer" label="Percent length required for an allele match [default 50]" value="50" />
     
     </inputs>
     <outputs>