# HG changeset patch
# User jpetteng
# Date 1515531027 18000
# Node ID 3e42024d27baea107abf60412a4a4306fad2f7c3
# Parent  71af8383215874d75af1e59f930dd5fdb25970c4
Uploaded

diff -r 71af83832158 -r 3e42024d27ba ectyper.xml
--- a/ectyper.xml	Tue Jan 09 15:29:45 2018 -0500
+++ b/ectyper.xml	Tue Jan 09 15:50:27 2018 -0500
@@ -20,7 +20,15 @@
       #else if $jobtype.select == "pe"
         -i sample_1.fastq sample_2.fastq
       #end if
-      -b $maptype.select;
+
+	  #if $options.percent_identity
+	      -d  $options.percent_identity
+	  #end if
+
+	  #if $options.percent_length
+		  -l $options.percent_length
+	  #end if
+	  
       cat  ectyper_result*/ectyper_result.txt > results.txt; 
 
     ]]></command>
@@ -43,30 +51,23 @@
         </when>
       </conditional>
 
-      <conditional name="maptype">
-        <param name="select" type="select" label="Algorithms for BWA mapping?">
-          <option value="sam">sam</option>
-          <option value="mem">mem</option>
-        </param>
+      <conditional name="options">
+        <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"/>
       </conditional>
     
-
     </inputs>
     <outputs>
       <data format="txt" label="ectyper Results" name="results" from_work_dir="results.txt"/>
     </outputs>
-    <tests>
-       <test>
-         <output name="results" file="results.txt"/>
-       </test>
-    </tests>
+
     <help><![CDATA[
     
 **Usage: ectyper**
 
 **INPUT**
 
-A fasta assembly
+A fasta assembly or single or paired end reads
 
 **PERCENTIDENTITY**
 
@@ -76,15 +77,7 @@
 
 Percentage of length wanted to use against the database. From 0 to 100, default is 50%.
 
-**verify**
-
-Enable E. Coli. verification
+https://github.com/phac-nml/ecoli_serotyping
 
-**species**
-
-Enable species identification when non-ecoli genome is found Note: refseq downloading is required when running this option for the first time.
-
-**OUTPUT**
-Directory location of output files.
     ]]></help>
 </tool>