--- a/hicup_truncater.xml	Fri May 25 17:50:43 2018 -0400
+++ b/hicup_truncater.xml	Sat Oct 22 08:37:07 2022 +0000
@@ -1,67 +1,94 @@
-<tool id="hicup_truncater" name="Hicup Truncater" version="@VERSION@.0">
+<tool id="hicup_truncater" name="Hicup Truncater" version="@VERSION@+galaxy0">
     <description>terminates sequence reads at specified Hi-C ligation junctions.</description>
     <macros>
         <import>hicup_macros.xml</import>
     </macros>
-    <expand macro="requirements_hicup" />
+    <expand macro="requirements_hicup"/>
     <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
+        ##Dealing with inputs
+        @PAIRED-END_INPUT@
         
-        #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
-        $input1 $input2
+        hicup_truncater --re1 '$re1' --zip $advanced_options.nofill
+            '$read1'
+            '$read2'
     ]]></command>
     <inputs>
-        <expand macro="input_files" />
-        <expand macro="re1" />
+        <expand macro="input_paired"/>
+        <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"/>
+            <expand macro="no_fill"/>
         </section>
     </inputs>
     <outputs>
-        <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" />
+        <data name="dataset1_trunc" format="fastq.gz" label="Hicup Truncation on ${on_string}: Read 1 Output" from_work_dir="dataset1*.trunc.fastq.gz">
+            <filter>library['type'] != 'paired_collection'</filter>
+        </data>
+        <data name="dataset2_trunc" format="fastq.gz" label="Hicup Truncation on ${on_string}: Read 2 Output" from_work_dir="dataset2*.trunc.fastq.gz">
+            <filter>library['type'] != 'paired_collection'</filter>
+        </data>
+        <collection name="dataset_trunc_pairs" type="paired" format="fastq.gz" label="Hicup Truncation on ${on_string}">
+            <filter>library['type'] == 'paired_collection' and 'multiple_output' not in output_selector</filter>
+            <data name="forward" from_work_dir="dataset1*.trunc.fastq.gz"/>
+            <data name="reverse" from_work_dir="dataset2*.trunc.fastq.gz"/>
+        </collection>
+        <data name="hicup_truncater_summary" format="tabular" label="hicup_truncater_summary.txt" from_work_dir="hicup_truncater_summary*.txt"/>
+        <collection type="list" name="truncation_barchart" label="Truncation Barchart.svg">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.truncation_barchart\.svg$" directory="./" ext="svg"/>
+        </collection>
     </outputs>
     <tests>
         <test>
-            <param name="input_first_sequence" value="dataset1.fastq" ftype="fastq"/>
-            <param name="input_second_sequence" value="dataset2.fastq" ftype="fastq"/>
+            <conditional name="library">
+                <param name="type" value="paired"/>
+                <param name="input_1" value="dataset1.fastq" ftype="fastq"/>
+                <param name="input_2" value="dataset2.fastq" ftype="fastq"/>
+            </conditional>
             <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.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" />
+            <output name="hicup_truncater_summary">
+                <assert_contents>
+                    <has_text_matching expression="\s+99742\s+7230\s+7.25\s+92512\s+92.75\s+22.45"/>
+                    <has_text_matching expression="\s+99742\s+7114\s+7.13\s+92628\s+92.87\s+22.63"/>
+                </assert_contents>
+            </output>
+            <output name="dataset1_trunc" file="dataset1.trunc.fastq.gz" decompress="true"/>
+            <output name="dataset2_trunc" file="dataset2.trunc.fastq.gz" decompress="true"/>
+            <output_collection name="truncation_barchart" count="2">
+                <element name="dataset1.fq" file="dataset1.truncation_barchart.svg" ftype="svg" compare="sim_size"/>
+                <element name="dataset2.fq" file="dataset2.truncation_barchart.svg" ftype="svg" compare="sim_size"/>
+            </output_collection>
+        </test>
+        <test>
+            <conditional name="library">
+                <param name="type" value="paired_collection"/>
+                <param name="input_1">
+                    <collection type="paired">
+                        <element name="forward" ftype="fastq" value="dataset1.fastq"/>
+                        <element name="reverse" ftype="fastq" value="dataset2.fastq"/>
+                    </collection>
+                </param>
+            </conditional>
+            <param name="re1" value="A^AGCTT"/>
+            <output name="hicup_truncater_summary">
+                <assert_contents>
+                    <has_text_matching expression="\s+99742\s+7230\s+7.25\s+92512\s+92.75\s+22.45"/>
+                    <has_text_matching expression="\s+99742\s+7114\s+7.13\s+92628\s+92.87\s+22.63"/>
+                </assert_contents>
+            </output>
+            <output_collection name="dataset_trunc_pairs" type="paired" count="2">
+                <element name="forward" decompress="true" file="dataset1.trunc.fastq.gz" ftype="fastq.gz"/>
+                <element name="reverse" decompress="true" file="dataset2.trunc.fastq.gz" ftype="fastq.gz"/>
+            </output_collection>
+            <output_collection name="truncation_barchart" count="2">
+                <element name="dataset1.fq" file="dataset1.truncation_barchart.svg" ftype="svg" compare="sim_size"/>
+                <element name="dataset2.fq" file="dataset2.truncation_barchart.svg" ftype="svg" compare="sim_size"/>
+            </output_collection>
         </test>
     </tests>
     <help><![CDATA[
 
-    For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/
+    For help please consult the documentation of HiCUP: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html
 
-    To get more information about the truncater visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Truncater
+    To get more information about the truncater visit: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html#hicup-truncater
     ]]></help>
-
-   <expand macro="citation_hicup" />
+    <expand macro="citation_hicup"/>
 </tool>