--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicup_truncater.xml	Thu Mar 09 09:32:44 2017 -0500
@@ -0,0 +1,58 @@
+<tool id="hicup_truncater" name="Hicup Truncater" version="0.1.0">
+    <description>terminates sequence reads at specified Hi-C ligation junctions.</description>
+    <macros>
+        <import>hicup_macros.xml</import>
+    </macros>
+    <expand macro="requirements_hicup" />
+    <expand macro="stdio" />
+    <command><![CDATA[
+        hicup_truncater --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
+        
+    ]]></command>
+    <inputs>
+        <expand macro="input_files" />
+        <expand macro="re1" />
+        <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" />
+
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_first_sequence" value="dataset1.fastq" ftype="fastq"/>
+            <param name="input_second_sequence" value="dataset2.fastq" ftype="fastq"/>
+            <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_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>
+    </tests>
+    <help><![CDATA[
+
+    For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/
+
+    To get more information about the truncater visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Truncater
+    ]]></help>
+
+   <expand macro="citation_hicup" />
+</tool>