# HG changeset patch
# User estrain
# Date 1567900069 14400
# Node ID 526617c6f359e9f2aa50260536f578ed318847d6
# Parent  f918518b7d7b191c7654112021d21b13bf018993
Uploaded

diff -r f918518b7d7b -r 526617c6f359 seqsero2.xml
--- a/seqsero2.xml	Sat Sep 07 19:47:33 2019 -0400
+++ b/seqsero2.xml	Sat Sep 07 19:47:49 2019 -0400
@@ -18,33 +18,50 @@
         #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
         #set $forward = $reads.forward
         #set $reverse = $reads.reverse
-      #else
+        #set $infile = $name + "_1.fastq " +  $name + "_2.fastq" 
+        #set $tval = 2
+        #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
+          gunzip -c $reverse > reverse.fastq;
+          #set $reverse = './reverse.fastq'
+          gunzip -c $forward > forward.fastq;
+          #set $forward = './forward.fastq'
+        #end if
+        ln -s $forward ${name}_1.fastq;
+        ln -s $reverse ${name}_2.fastq;
+      #else if $reads.reads_select == 'collection'
         #set $name = $reads.coll.name.replace(' ', '_')
         #set $forward = $reads.coll.forward
         #set $reverse = $reads.coll.reverse
+        #set $infile = $name + "_1.fastq " +  $name + "_2.fastq" 
+        #set $tval = 2
+        #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
+          gunzip -c $reverse > reverse.fastq;
+          #set $reverse = './reverse.fastq'
+          gunzip -c $forward > forward.fastq;
+          #set $forward = './forward.fastq'
+        #end if
+        ln -s $forward ${name}_1.fastq;
+        ln -s $reverse ${name}_2.fastq;
+      #else 
+        #set $name = $reads.assembly.name.replace(' ', '_')
+        #set $ga = $reads.assembly
+        #set $infile = $name + ".fasta" 
+        ln -s $ga ${name}.fasta;
+        #set $tval = 4
+        #set $mode='k'
       #end if
       echo $name ;
       echo "-=-=-=-=-" ;
-      #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz')
-        gunzip -c $forward > forward.fastq;
-        #set $forward = './forward.fastq'
-      #end if
-      #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
-        gunzip -c $reverse > reverse.fastq;
-        #set $reverse = './reverse.fastq'
-      #end if
-      ln -s $forward ${name}_1.fastq;
-      ln -s $reverse ${name}_2.fastq;
       touch output/SeqSero_log.txt ;
       python $__tool_directory__/SeqSero2_package.py
         -p \${GALAXY_SLOTS:-4}
-        -t 2
+        -t $tval 
         -m $mode
         -d ./output
       #if $mode == 'a':
         -b $maptype 
       #end if
-        -i ${name}_1.fastq ${name}_2.fastq &&
+        -i $infile &&
         echo "-=-=-=-=-" &&
         cat output/SeqSero_log.txt &&
         echo "-=-=-=-=-" &&
@@ -53,9 +70,10 @@
     <inputs>
         
         <conditional name="reads">
-            <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
+            <param name="reads_select" type="select" label="Genome assembly,paired-end collection, or two datasets from your history">
                 <option value="collection">Paired collection from your history</option>
                 <option value="history">Two FASTQ datasets from your history</option>
+                <option value="genome">Genome Assembly</option>
             </param>
             <when value="collection">
                 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
@@ -64,6 +82,9 @@
                 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
                 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
             </when>
+            <when value="genome">
+                <param label="Genome assembly" name="assembly" type="data" format="fasta"/>
+            </when>
         </conditional>
      
           <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
@@ -77,7 +98,7 @@
         
         <param label="Analysis mode" type="select" name="mode">
          <option value="a">allele mode</option>
-            <option value="k">k-mer mode</option>
+         <option value="k">k-mer mode</option>
         </param>
 
         <param name="maptype" type="select" label="Algorithms for BWA mapping">