--- a/bwameth.xml	Sun Mar 12 04:11:22 2017 -0400
+++ b/bwameth.xml	Tue Apr 11 09:19:24 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="bwameth" name="bwameth" version="0.2.0.2">
+<tool id="bwameth" name="bwameth" version="0.2.0.3" profile="17.01">
     <description>Fast and accurate aligner of BS-Seq reads.</description>
     <requirements>
         <requirement type="package" version="1.2">samtools</requirement>
@@ -16,6 +16,55 @@
         #set index=$referenceSource.index.fields.path
     #end if
 
+    ## Link in the files with a name that's appropriate
+    #if str($single_or_paired.single_or_paired_opts) == 'paired':
+        #if $single_or_paired.input_mate1.is_of_type("fastq.gz", "fastqsanger.gz"):
+            #set read1 = "input_f.fastq.gz"
+        #else if $single_or_paired.input_mate1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+            #set read1 = "input_f.fastq.bz2"
+        #else:
+            #set read1 = "input_f.fastq"
+        #end if
+        ln -f -s '${single_or_paired.input_mate1}' ${read1} &&
+
+        #if $single_or_paired.input_mate2.is_of_type("fastq.gz", "fastqsanger.gz"):
+            #set read2 = "input_r.fastq.gz"
+        #else if $single_or_paired.input_mate2.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+            #set read2 = "input_r.fastq.bz2"
+        #else:
+            #set read2 = "input_r.fastq"
+        #end if
+        ln -f -s '${single_or_paired.input_mate2}' ${read2} &&
+    #else if str($single_or_paired.single_or_paired_opts) == 'paired_collection':
+        #if $single_or_paired.input_mate1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
+            #set read1 = "input_f.fastq.gz"
+        #else if $single_or_paired.input_mate1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+            #set read1 = "input_f.fastq.bz2"
+        #else:
+            #set read1 = "input_f.fastq"
+        #end if
+        ln -s '${single_or_paired.input_mate1.forward}' ${read1} &&
+
+        #if $single_or_paired.input_mate1.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
+            #set read2 = "input_r.fastq.gz"
+        #else if $single_or_paired.input_mate1.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+            #set read2 = "input_r.fastq.bz2"
+        #else:
+            #set read2 = "input_r.fastq"
+        #end if
+        ln -s '${single_or_paired.input_mate1.reverse}' ${read2} &&
+    #else:
+        #if $single_or_paired.input_singles.is_of_type("fastq.gz", "fastqsanger.gz"):
+            #set read1 = "input_f.fastq.gz"
+        #else if $single_or_paired.input_singles.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+            #set read1 = "input_f.fastq.bz2"
+        #else:
+            #set read1 = "input_f.fastq"
+        #end if
+        ln -f -s '${single_or_paired.input_singles}' ${read1} &&
+    #end if
+
+
     bwameth.py
         -t "\${GALAXY_SLOTS:-4}"
         --reference "${index}"
@@ -25,11 +74,9 @@
     #end if
 
     #if $single_or_paired.single_or_paired_opts == 'single':
-        $single_or_paired.input_singles
-    #elif $single_or_paired.single_or_paired_opts == 'paired':
-        $single_or_paired.input_mate1 $single_or_paired.input_mate2
+        $read1
     #else:
-        $single_or_paired.input_mate1.forward $single_or_paired.input_mate1.reverse
+        $read1 $read2
     #end if
     | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o output.bam -
 ]]>
@@ -60,14 +107,14 @@
                 <option value="paired_collection">Paired-end Dataset Collection</option>
             </param>
             <when value="single">
-                <param name="input_singles" type="data" format="fastqsanger" label="FASTQ" help="FASTQ file." />
+                <param name="input_singles" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="FASTQ" help="FASTQ file." />
             </when>
             <when value="paired">
-                <param name="input_mate1" type="data" format="fastqsanger" label="First read in pair" help="FASTQ file." />
-                <param name="input_mate2" type="data" format="fastqsanger" label="Second read in pair" help="FASTQ file." />
+                <param name="input_mate1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="First read in pair" help="FASTQ file." />
+                <param name="input_mate2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Second read in pair" help="FASTQ file." />
             </when>
             <when value="paired_collection">
-                <param name="input_mate1" type="data_collection" collection_type="paired" format="fastqsanger" label="FASTQ paired dataset" help="Must have a fastqsanger datatype." />
+                <param name="input_mate1" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="FASTQ paired dataset" help="Must have a fastqsanger datatype." />
             </when>
         </conditional>
         <param name="readGroup" type="text" value="" label="Read group" help="If desired, you can manually add read group information to the resulting BAM file. To do so, you MUST manually specify the entire string, such as '@RG\tID:foo\tSM:bar'">
@@ -82,8 +129,8 @@
             <param name="referenceSource" value="history" />
             <param name="reference" value="ref.fa.gz" />
             <param name="single_or_paired_opts" value="paired" />
-            <param name="input_mate1" value="t_R1.fastq.gz" />
-            <param name="input_mate2" value="t_R2.fastq.gz" />
+            <param name="input_mate1" value="t_R1.fastq.gz"/>
+            <param name="input_mate2" value="t_R2.fastq.gz"/>
             <output file="output.bam" ftype="bam" name="output" lines_diff="2"/>
         </test>
         <test>
@@ -92,8 +139,8 @@
             <param name="single_or_paired_opts" value="paired_collection" />
             <param name="input_mate1">
                 <collection type="paired">
-                    <element name="forward" value="t_R1.fastq.gz" />
-                    <element name="reverse" value="t_R2.fastq.gz" />
+                    <element name="forward" value="t_R1.fastq.gz"/>
+                    <element name="reverse" value="t_R2.fastq.gz"/>
                 </collection>
             </param>
             <output file="output.bam" ftype="bam" name="output" lines_diff="2"/>