--- a/ecoli_serotyping/ectyper.xml	Fri Jan 05 09:17:33 2018 -0500
+++ b/ecoli_serotyping/ectyper.xml	Fri Jan 05 10:00:07 2018 -0500
@@ -11,34 +11,55 @@
 #      <requirement type="package">mash</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-     
-      ln -s $fasta1 sample_1.fastq;  
-      ln -s $fastq2 sample_2.fastq;  
+      #if $jobtype.select == "asm"
+        ln -s $jobtype.draft sample.fasta;  
+      #else if $jobtype.select == "se"
+        ln -s $jobtype.fastq1 sample_1.fastq;  
+      #else if $jobtype.select == "pe"
+        ln -s $jobtype.fastq1 sample_1.fastq;  
+        ln -s $jobtype.fastq2 sample_2.fastq;  
+      #end if
 
       $__tool_directory__/ectyper.py
-      -i ecoliA.fasta for a single file
-      -i ecoliA.fasta,ecoliB.fastq,ecoliC.fna for multiple files
-      -i ecoli_folder for a folder
-      -i ecoli_folder for a folder
-      -d PERCENTIDENTITY
-      -l PERCENTLENGTH
-      -o OUTPUT; 
+      #if $jobtype.select == "asm"
+        -m 4
+        -i sample.fasta
+      #else if $jobtype.select == "se"
+        -m 3
+        -i sample_1.fastq
+      #else if $jobtype.select == "pe"
+        -m 2
+        -i sample_1.fastq sample_2.fastq
+      #end if
+      -b $maptype.select;
       cat  SeqSero_result*/Seqsero_result.txt > results.txt; 
 
     ]]></command>
     <inputs>
-          <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
-          <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" />
-          <param name="numofthr" type="select" label="Number of threads">
-          <option value="1">1</option>
-          <option value="2">2</option>
-          <option value="3">3</option>
-          <option value="4">4</option>
+      <conditional name="jobtype">
+        <param name="select" type="select" label="Assembly or FASTQ Reads?">
+          <option value="asm">Genome Assembly</option>
+          <option value="se">Single-End Reads</option>
+          <option value="pe">Paired-End Reads</option>
         </param>
-        <param name="maptype" type="select" label="Algorithms for BWA mapping?">
+        <when value="asm">
+          <param name="draft" type="data" format="fasta" label="FASTA" />
+        </when>
+        <when value="se">
+          <param name="fastq1" type="data" format="fastq" label="FASTQ" />
+        </when>
+        <when value="pe">
+          <param name="fastq1" type="data" format="fastq" label="FASTQ" />
+          <param name="fastq2" type="data" format="fastq" label="FASTQ" />
+        </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>
-          <option value="sam">sam</option>
         </param>
+      </conditional>
     
 
     </inputs>
@@ -56,7 +77,7 @@
 
 **INPUT**
 
-Location of new file(s). Can be a single file or a directory
+A fasta assembly
 
 **PERCENTIDENTITY**