--- a/seqsero2.xml	Tue Nov 06 09:45:57 2018 -0500
+++ b/seqsero2.xml	Fri Nov 09 11:30:45 2018 -0500
@@ -1,25 +1,26 @@
 <tool id="seqsero_v2" name="SeqSero 2" version="2.0">
     <description>Salmonella serotype prediction</description>
     <requirements>
-      <requirement type="package" version="2.7.10">python</requirement>
-      <requirement type="package" version="1.60">biopython</requirement>
-      <requirement type="package" version="2.2.31">blast</requirement>
+      <requirement type="package" version="3.6">python</requirement>
+      <requirement type="package" version="1.70">biopython</requirement>
+      <requirement type="package" version="2.7.1">blast</requirement>
       <requirement type="package" version="1.9">samtools</requirement>
-      <requirement type="package" version="2.6.2">sra-tools</requirement>
+      <requirement type="package" version="2.9.1">sra-tools</requirement>
       <requirement type="package" version="0.7.17">bwa</requirement>
-      <requirement type="package" version="3.9.0">spades</requirement>
+      <requirement type="package" version="3.12.0">spades</requirement>
       <requirement type="package" version="2.27.1">bedtools</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
       #if $reads.reads_select == 'history'
-      #set name = $reads.forward.name.split('_')[0]
+      #set name = $reads.forward.name.split('.')[0].replace(' ','_')
       #set forward = $reads.forward
       #set reverse = $reads.reverse
       #else
-      #set name = $reads.coll.name
+      #set name = $reads.coll.name.replace(' ', '_')
       #set forward = $reads.coll.forward
       #set reverse = $reads.coll.reverse
       #end if
+      echo $name ;
       #if forward.is_of_type('fastq.gz', 'fastqsanger.gz')
       gunzip -c $forward > forward.fastq;
       #set forward = './forward.fastq'
@@ -30,15 +31,25 @@
       #end if
       ln -s forward.fastq ${name}_1.fastq;
       ln -s reverse.fastq ${name}_2.fastq;
-      $__tool_directory__/SeqSero2.py
+      mkdir ./output;
+      python $__tool_directory__/SeqSero2/SeqSero2_package.py
       -p \${GALAXY_SLOTS:-4}
-      -i ${name}_1.fastq ${name}_2.fastq
-      -b $maptype && 
-      cat  SeqSero_result*/Seqsero_result.tsv > results.tsv 
-
+      -t 2
+      -m $mode
+      -d ./output
+      -b $maptype 
+      -i ${name}_1.fastq ${name}_2.fastq &&
+      echo "-=-=-=-=-" &&
+      cat output/SeqSero_log.txt &&
+      echo "-=-=-=-=-" &&
+      ls -lah ./output
     ]]></command>
     <inputs>
       
+        <param label="Analysis mode" type="select" name="mode">
+            <option value="k">k-mer mode</option>
+            <option value="a">allele mode</option>
+        </param>
         
         <conditional name="reads">
             <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
@@ -70,15 +81,34 @@
 
     </inputs>
     <outputs>
-      <data format="tsv" label="SeqSero Results" name="results" from_work_dir="results.tsv"/>
+      <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/Seqsero_result.tsv"/>
     </outputs>
     <tests>
+       <!-- <test>
+         <param name="reads_select" value="history" />
+         <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
+         <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
+         <output name="results" file="Seqsero_result.tsv" />
+       </test>
        <test>
+        <param name="reads_select" value="collection" />
+        <param name="coll">
+            <collection type="paired">
+                <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
+                <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
+            </collection>
+        </param>
+        <output name="results" file="Seqsero_result.tsv" />
+       </test> -->
+        <test>
+         <param name="mode" value="k" />
          <param name="reads_select" value="history" />
          <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
          <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
+         <output name="results" file="Seqsero_result_25k.tsv" />
        </test>
        <test>
+        <param name="mode" value="k" />
         <param name="reads_select" value="collection" />
         <param name="coll">
             <collection type="paired">
@@ -86,7 +116,19 @@
                 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
             </collection>
         </param>
+        <output name="results" file="Seqsero_result_25k_coll.tsv" />
        </test>
+       <!-- <test>
+        <param name="mode" value="a" />
+        <param name="reads_select" value="collection" />
+        <param name="coll">
+            <collection type="paired">
+                <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
+                <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
+            </collection>
+        </param>
+        <output name="results" file="Seqsero_result_allele.tsv" />
+       </test> -->
     </tests>
     <help><![CDATA[