--- a/hicup_filter.xml	Thu Nov 09 11:16:04 2017 -0500
+++ b/hicup_filter.xml	Fri May 25 17:49:27 2018 -0400
@@ -1,59 +1,64 @@
-<tool id="hicup_filter" name="Hicup Filter" version="@VERSION@.0">
-    <description>classifies read pairs, identifying valid Hi-C di-tags.</description>
+<tool id="hicup_filter" name="Hicup Filter" version="@VERSION@.0" profile="18.01">
+    <description>classifies read pairs, identifying valid Hi-C di-tags</description>
     <macros>
         <import>hicup_macros.xml</import>
     </macros>
-    <expand macro="requirements_hicup" />
-    <expand macro="stdio" />
-    <command><![CDATA[    
-        hicup_filter --digest '$digest'
+    <expand macro="requirements_hicup"/>
+    <command detect_errors="exit_code"><![CDATA[
+        #for $i, $file in enumerate($inputFiles):
+            #if $file.ext != 'sam':
+                ln -s '$file' ./${i}.bam  &&
+            #end if
+        #end for
+        hicup_filter --zip --digest '$digest'
         #if $advanced_options.longest:
             --longest '$advanced_options.longest'
         #end if
         #if $advanced_options.shortest:
             --shortest '$advanced_options.shortest'
         #end if
-        #for $file in $inputFiles:
-            $file
+        #for $i, $file in enumerate($inputFiles):
+            #if $file.ext != 'sam':
+                ./${i}.bam
+            #else:
+                '$file'
+            #end if
         #end for
-        && mv hicup_filter_ditag_rejects* hicup_filter_ditag_rejects
-        && mv *filt.sam dataset.filt.sam
-        && mv hicup_filter_summary* hicup_filter_summary.txt
-        && mv hicup_filter_ditag_rejects/*contiguous.filter.sam hicup_filter_ditag_rejects/dataset.contiguous.filter.sam
-        && mv hicup_filter_ditag_rejects/*re_ligation.filter.sam  hicup_filter_ditag_rejects/dataset.re_ligation.filter.sam 
-        && mv hicup_filter_ditag_rejects/*same_dangling_ends.filter.sam hicup_filter_ditag_rejects/dataset.same_dangling_ends.filter.sam
-        && mv hicup_filter_ditag_rejects/*invalid.filter.sam hicup_filter_ditag_rejects/dataset.invalid.filter.sam 
-        && mv hicup_filter_ditag_rejects/*same_circularised.filter.sam hicup_filter_ditag_rejects/dataset.same_circularised.filter.sam
-        && mv hicup_filter_ditag_rejects/*same_internal.filter.sam hicup_filter_ditag_rejects/dataset.same_internal.filter.sam
-        #if $advanced_options.longest or $advanced_options.shortest: 
-        && mv hicup_filter_ditag_rejects/*wrong_size.filter.sam hicup_filter_ditag_rejects/dataset.wrong_size.filter.sam
-        #end if
-       
-        && mv *filter_piechart.svg filter_piechart.svg
     ]]></command>
     <inputs>
-        <param name="inputFiles" type="data" multiple="true" format="bam,sam" label="Input"/>
+        <param name="inputFiles" type="data" multiple="true" format="sam,qname_sorted.bam" label="Input files in BAM or SAM fomat"/>
         <param argument="--digest" type="data" format="txt" label="Genome digest file" help="Specify the genome digest file (created by hicup_digester)"/>
         <section name="advanced_options" title="Advanced options">
             <expand macro="filter_longest_shortest" />
         </section>
     </inputs>
     <outputs>
-        <expand macro="filter_output" />
+        <data name="dataset_filt" format="qname_sorted.bam" from_work_dir="*.filt.bam" label="filt.bam" />
+        <data name="hicup_filter_summary" format="txt" from_work_dir="hicup_filter_summary*.txt" label="hicup_filter_summary.txt" />
+        <data name="contiguous_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*contiguous.filter.bam" label="contiguous.filter.bam" />
+        <data name="re_ligation_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*re_ligation.filter.bam" label="re_ligation.filter.bam" />
+        <data name="same_dangling_ends_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*same_dangling_ends.filter.bam" label="same_dangling_ends.filter.bam" />
+        <data name="invalid_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*invalid.filter.bam" label="invalid.filter.bam" />
+        <data name="same_circularised_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*same_circularised.filter.bam" label="same_circularised.filter.bam" />
+        <data name="same_internal_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*same_internal.filter.bam" label="same_internal.filter.bam" />
+        <data name="wrong_size_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*wrong_size.filter.bam" label="wrong_size.filter.bam"/>
+        <data name="filter_piechart" format="svg" from_work_dir="*filter_piechart.svg" label="Filter piechart" />
+        <data name="ditag_size_distribution" format="svg" from_work_dir="*.ditag_size_distribution.svg" label="Ditag size distribution" />
     </outputs>
     <tests>
         <test>
+            <param name="inputFiles" value="dataset1_2.pair.bam" ftype="qname_sorted.bam" />
             <param name="digest" value="digester_file.txt" ftype="txt" />
-            <param name="inputFiles" value="result.pair.sam" ftype="sam" />
             <output name="hicup_filter_summary" file="hicup_filter_summary.txt" lines_diff="12"/>
-            <output name="dataset_filt" file="dataset.filt.sam" lines_diff="8" />
-            <output name="contiguous_filter" file="dataset.contiguous.filter.sam" lines_diff="8" />
-            <output name="re_ligation_filter" file="dataset.re_ligation.filter.sam" lines_diff="8" />
-            <output name="same_dangling_ends_filter" file="dataset.same_dangling_ends.filter.sam" lines_diff="8" />
-            <output name="invalid_filter" file="dataset.invalid.filter.sam"  lines_diff="8" />
-            <output name="same_circularised_filter" file="dataset.same_circularised.filter.sam" lines_diff="8" />
-            <output name="same_internal_filter" file="dataset.same_internal.filter.sam" lines_diff="8" />
-            <output name="filter_piechart" file="filter_piechart.svg" ftype="svg" lines_diff="1000" />
+            <output name="dataset_filt" file="dataset1_2.filt.bam" lines_diff="8" ftype="qname_sorted.bam" />
+            <output name="contiguous_filter" file="dataset1_2_contiguous.filter.bam" lines_diff="8" ftype="qname_sorted.bam" />
+            <output name="re_ligation_filter" file="dataset1_2_re_ligation.filter.bam" lines_diff="8" ftype="qname_sorted.bam" />
+            <output name="same_dangling_ends_filter" file="dataset1_2_same_dangling_ends.filter.bam" lines_diff="8" ftype="qname_sorted.bam" />
+            <output name="invalid_filter" file="dataset1_2_invalid.filter.bam"  lines_diff="8" ftype="qname_sorted.bam" />
+            <output name="same_circularised_filter" file="dataset1_2_same_circularised.filter.bam" lines_diff="8" ftype="qname_sorted.bam" />
+            <output name="same_internal_filter" file="dataset1_2_same_internal.filter.bam" lines_diff="8" ftype="qname_sorted.bam" />
+            <output name="filter_piechart" file="dataset1_2.pair.bam.filter_piechart.svg" ftype="svg" lines_diff="1000" />
+            <output name="ditag_size_distribution" file="dataset1_2.ditag_size_distribution.svg" ftype="svg" lines_diff="1000" />
         </test>
     </tests>
     <help><![CDATA[