--- a/hicup_truncater.xml	Thu Nov 09 11:16:43 2017 -0500
+++ b/hicup_truncater.xml	Fri May 25 17:50:43 2018 -0400
@@ -4,35 +4,44 @@
         <import>hicup_macros.xml</import>
     </macros>
     <expand macro="requirements_hicup" />
-    <expand macro="stdio" />
-    <command><![CDATA[
-        hicup_truncater --re1 '$re1' $advanced_options.nofill 
+    <command detect_errors="exit_code"><![CDATA[
+        ##Dealing with fastq and fastq.gz
+        #if $input_first_sequence.is_of_type("fastq.gz", "fastqsanger.gz"):
+           ln -s $input_first_sequence dataset1.gz &&
+           #set input1='dataset1.gz'
+        #else
+           ln -s $input_first_sequence dataset1 &&
+           #set input1='dataset1'
+        #end if
+        
+        #if $input_second_sequence.is_of_type("fastq.gz", "fastqsanger.gz"):
+            ln -s $input_second_sequence dataset2.gz &&
+            #set input2='dataset2.gz'
+        #else
+            ln -s $input_second_sequence dataset2 &&
+            #set input2='dataset2'
+        #end if
+        
+        hicup_truncater --zip --re1 '$re1' $advanced_options.nofill 
         #if $advanced_options.sequences:
             --sequences '$advanced_options.sequences'
         #end if
-        '$input_first_sequence' '$input_second_sequence'
-
-        && mv hicup_truncater_summary* hicup_truncater_summary.txt
-        && trunc_result_1=\$(echo '$input_first_sequence' | rev | cut -d'/' -f1 | rev)
-      
-        && mv \$trunc_result_1.trunc.fastq dataset1.trunc.fastq
-        && trunc_result_2=\$(echo '$input_second_sequence' | rev | cut -d'/' -f1 | rev)
-        && mv \$trunc_result_2.trunc.fastq dataset2.trunc.fastq
-        && mv \$trunc_result_1.truncation_barchart.svg dataset1.truncation_barchart.svg
-        && mv \$trunc_result_2.truncation_barchart.svg dataset2.truncation_barchart.svg
-        
+        $input1 $input2
     ]]></command>
     <inputs>
         <expand macro="input_files" />
         <expand macro="re1" />
-        <section name="advanced_options" title="Advanced options">   
-            <expand macro="no_fill" />     
+        <section name="advanced_options" title="Advanced options">
+            <expand macro="no_fill" />
             <param argument="--sequences" type="text" value="" label="Ligation sequence" help="Instead of specifying a restriction enzyme recognition sequence, specify the ligation sequences directly"/>
         </section>
     </inputs>
     <outputs>
-       <expand macro="truncater_output" />
-
+        <data name="hicup_truncater_summary" format="txt" label="hicup_truncater_summary.txt" from_work_dir="hicup_truncater_summary*.txt" />
+        <data name="dataset1_trunc" format="fastq.gz" label="Hicup Dataset1 Truncation" from_work_dir="dataset1*.trunc.fastq.gz" />
+        <data name="dataset2_trunc" format="fastq.gz" label="Hicup Dataset2 Truncation" from_work_dir="dataset2*.trunc.fastq.gz" />
+        <data name="dataset1_truncater_barchart" format="svg" label="Hicup Dataset1 Truncation Barchart.svg" from_work_dir="dataset1*.truncation_barchart.svg" />
+        <data name="dataset2_truncater_barchart" format="svg" label="Hicup Dataset2 Truncation Barchart.svg" from_work_dir="dataset2*.truncation_barchart.svg" />
     </outputs>
     <tests>
         <test>
@@ -41,8 +50,8 @@
             <param name="re1" value="A^AGCTT"/>
             
             <output name="hicup_truncater_summary" file="hicup_truncater_summary.txt" lines_diff="8"/>
-            <output name="dataset1_trunc" file="dataset1.trunc.fastq" lines_diff="8" />
-            <output name="dataset2_trunc" file="dataset2.trunc.fastq" lines_diff="8"/>
+            <output name="dataset1_trunc" file="dataset1.trunc.fastq.gz" compare="sim_size"/>
+            <output name="dataset2_trunc" file="dataset2.trunc.fastq.gz" compare="sim_size"/>
             <output name="dataset1_truncater_barchart" file="dataset1.truncation_barchart.svg" ftype="svg" lines_diff="1000" />
             <output name="dataset2_truncater_barchart" file="dataset2.truncation_barchart.svg" ftype="svg" lines_diff="1000" />
         </test>