--- a/hicBuildMatrix.xml	Fri Dec 11 21:04:27 2020 +0000
+++ b/hicBuildMatrix.xml	Tue Mar 16 15:12:54 2021 +0000
@@ -1,40 +1,45 @@
-<tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>create a contact matrix</description>
     <macros>
         <token name="@BINARY@">hicBuildMatrix</token>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" >
+    <expand macro="requirements">
         <requirement type="package" version="1.9">samtools</requirement>
     </expand>
     <command detect_errors="exit_code"><![CDATA[
 
         mkdir ./QCfolder &&
-        mkdir $qc.files_path &&
+        mkdir '$qc.files_path' &&
         @BINARY@
-
             --samFiles
             #for $repeat in $samFiles:
                 '${repeat.samFile}'
             #end for
 
-            #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionRestrictionCutFile":
-                --restrictionCutFile '$restrictionCutFileBinSize_conditional.restrictionCutFile'
-                --minDistance $restrictionCutFileBinSize_conditional.minDistance
-                --maxLibraryInsertSize $restrictionCutFileBinSize_conditional.maxLibraryInsertSize
+            --restrictionCutFile '$restrictionCutFile'
+            
+            #if $restrictionSequence:
+                --restrictionSequence '$restrictionSequence'
+            #end if
+            #if $danglingSequence:
+                --danglingSequence '$danglingSequence'
             #end if
-
-            #if $restrictionCutFileBinSize_conditional.restrictionCutFileBinSize_selector == "optionBinSize":
+            #if $minDistance:
+            --minDistance $minDistance
+            #end if
+            #if $maxLibraryInsertSize:
+                --maxLibraryInsertSize $maxLibraryInsertSize
+            #end if
+           
+            #if $binSizes:
                 --binSize
-                #for $repeat in $restrictionCutFileBinSize_conditional.binSizes
+                #for $repeat in $binSizes
                     '${repeat.binSize}'
                 #end for
             #end if
 
-
-            #if $restrictionSequence:
-                --restrictionSequence '$restrictionSequence'
-            #end if
+            --genomeAssembly $samFiles[0].samFile.metadata.dbkey
 
             #if $region:
                 --region '$region'
@@ -42,18 +47,20 @@
 
             --outFileName matrix.$outputFormat
 
-            #if $outBam_Boolean:
-                $outBam_Boolean ./unsorted.bam
+            #if $outBam:
+                $outBam ./unsorted.bam
             #end if
 
             $keepSelfCircles
+            $removeSelfLigation
+            $skipDuplicationCheck
 
             #if $minMappingQuality and $minMappingQuality is not None:
                 --minMappingQuality $minMappingQuality
             #end if
 
-            #if $danglingSequence:
-                --danglingSequence '$danglingSequence'
+            #if $chromosomeSizes:
+                --chromosomeSizes '$chromosomeSizes'
             #end if
 
             --threads @THREADS@
@@ -62,77 +69,57 @@
         &&
         mv ./QCfolder/* $qc.files_path/
         &&
-        mv $qc.files_path/hicQC.html $qc
-        && mv $qc.files_path/*.log raw_qc
+        mv '$qc.files_path/hicQC.html' '$qc'
+        && mv "$qc.files_path"/*.log raw_qc
         && mv matrix.$outputFormat matrix
-        #if $outBam_Boolean:
-            && samtools sort -T "\${TMPDIR:-.}" ./unsorted.bam -o sorted.bam
+        #if $outBam:
+            && samtools sort -@ @THREADS@ -T "\${TMPDIR:-.}" ./unsorted.bam -o sorted.bam
         #end if
-
 ]]>
     </command>
     <inputs>
-        <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)"
-                help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file.">
-            <param name="samFile" type="data" format="sam,qname_input_sorted.bam"/>
-        </repeat>
-        <conditional name="restrictionCutFileBinSize_conditional">
-            <param name="restrictionCutFileBinSize_selector" type="select" label="Choose to use a restriction cut file or a bin size">
-                <option value="optionRestrictionCutFile">Restriction cut file</option>
-                <option value="optionBinSize" selected="True">Bin size</option>
+        <!-- can we use multiple=True here with min="2" and max="2" ? -->
+        <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process (forward/reverse)" help="Please use the special BAM datatype: qname_input_sorted.bam and use for 'bowtie2' the '--reorder' option to create a BAM file.">
+            <param name="samFile" type="data" format="sam,qname_input_sorted.bam">
+                <validator type="unspecified_build" />
             </param>
-            <when value="optionRestrictionCutFile">
-                <param argument="--restrictionCutFile" type="data" format="bed" optional="true" label="BED file with all restriction cut places"
-                        help="Should contaion only  mappable restriction sites. If given, the bins are set to match the restriction fragments
-                        (i.e. the region between one restriction site and the next)." />
-                <param argument="--minDistance" type="integer" value="" optional="true" label="Minimum distance between restriction sites"
-                        help="Restriction sites that are closer that this distance are merged into one.
-                        This option only applies if --restrictionCutFile is given."/>
-                <param argument="--maxLibraryInsertSize" type="integer" value="" optional="true"
-                        label="Maximum library insert size defines different cut offs based on the maximum expected library size"
-                        help="*This is not the average fragment size* but the higher end of the fragment size distribution (obtained using for example Fragment Analyzer)
-                              which usually is between 800 to 1500 bp. If this value if not known use the default of 1000. The insert value is used to decide if two mates
-                              belong to the same fragment (by checking if they are within this max insert size) and to decide if a mate
-                              is too far away from the nearest restriction site." />
-            </when>
-            <when value="optionBinSize">
-                <repeat  name='binSizes' title='Bin size in bp' min="1" help="If used, the restriction cut places (if given) are used to only consider reads that are in the vicinity of the resctriction sites.
-                        Otherwise all reads in the interval are considered. Use multiple ones to create a mcool file.">
-                    <param argument="--binSize" type="integer" value="" optional="true" label="Bin size in bp"/>
-                </repeat>
-            </when>
-        </conditional>
+        </repeat>
+
+        <expand macro="restrictionCutFile" />
+        <expand macro="restrictionSequence" />
+        <expand macro="danglingSequence" />
 
-        <param argument="--restrictionSequence" type="text" optional="true" label="Sequence of the restriction site"
-            help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or
-            &quot;dangling-ends&quot;. If not given, such statistics will not be available." />
+        <param argument="--minDistance" type="integer" optional="true" value="" label="Minimum distance between restriction sites" help="Restriction sites that are closer that this distance are merged into one.
+                This option only applies if --restrictionCutFile is given." />
+        <param argument="--maxLibraryInsertSize" type="integer" optional="true" value="" label="Maximum library insert size defines different cut offs based on the maximum expected library size" help="*This is not the average fragment size* but the higher end of the fragment size distribution (obtained using for example Fragment Analyzer)
+                        which usually is between 800 to 1500 bp. If this value if not known use the default of 1000. The insert value is used to decide if two mates
+                        belong to the same fragment (by checking if they are within this max insert size) and to decide if a mate
+                        is too far away from the nearest restriction site." />
+
+        <repeat name='binSizes' title='Bin size in bp' min="1" help="If used, the restriction cut places (if given) are used to only consider reads that are in the vicinity of the resctriction sites.
+                Otherwise all reads in the interval are considered. Use multiple ones to create a mcool file.">
+            <param argument="--binSize" type="integer" optional="true" value="" label="Bin size in bp" />
+        </repeat>
 
         <expand macro="region" />
-
-        <param argument="--keepSelfCircles" type="boolean" truevalue="--keepSelfCircles" falsevalue=""
-            label="Keep self circles"
-            help="If set, outward facing reads without any restriction fragment (self circles) are kept. They will be counted and shown in the QC plots." />
-
+        <param argument="--keepSelfCircles" type="boolean" truevalue="--keepSelfCircles" falsevalue="" label="Keep self circles" help="If set, outward facing reads without any restriction fragment (self circles) are kept. They will be counted and shown in the QC plots." />
+        <param argument="--removeSelfLigation" type="boolean" truevalue="--removeSelfLigation" falsevalue="" label="remove self ligation" help="If set, inward facing reads less than 1000 bp apart and having a restriction site in between are removed. Although this reads do not contribute to any distant contact, they are useful to account for bias in the data" />
         <expand macro="minMappingQuality" />
+        <param argument="--skipDuplicationCheck" type="boolean" truevalue="--skipDuplicationCheck" falsevalue="" label="Skip duplication check" help="Identification of duplicated read pairs is memory consuming. Thus, in case of memory errors this check can be skipped." />
+        <param argument="--chromosomeSizes" type="data" format="tabular" optional="true" label="Chromosome sizes for your genome" help="File with the chromosome sizes for your genome. A tab-delimited two column layout 'chr_name size' is expected
+                    Usually the sizes can be determined from the SAM/BAM input files, however, 
+                    for cHi-C or scHi-C it can be that at the start or end no data is present. 
+                    Please consider that this option causes that only reads are considered which are on the listed chromosomes.
+                    Use this option to guarantee fixed sizes. An example file is available via UCSC: 
+                    http://hgdownload.soe.ucsc.edu/goldenPath/dm3/bigZips/dm3.chrom.sizes" />
 
-        <param argument="--danglingSequence" type="text" optional="true" label="Dangling sequence"
-            help="Sequence left by the restriction enzyme after cutting.
-                    Each restriction enzyme recognizes a different DNA sequence and,
-                    after cutting, they leave behind a specific ‘sticky’ end or dangling end sequence.
-                    For example, for HindIII the restriction site is AAGCTT and the dangling end is AGCT.
-                    For DpnII, the restriction site and dangling end sequence are the same: GATC.
-                    This information is easily found on the description of the restriction enzyme.
-                    The dangling sequence is used to classify and report reads whose 5’ end starts with such sequence as dangling-end reads.
-                    A significant portion of dangling-end reads in a sample are indicative of a problem with the re-ligation step of the protocol. "/>
-
-        <param name='outBam_Boolean' type='boolean' truevalue='--outBam'  falsevalue="" checked="false" label="Save valid Hi-C reads in BAM file"
-                    help="A bam
+        <param argument='--outBam' type='boolean' truevalue='--outBam' falsevalue="" checked="false" label="Save valid Hi-C reads in BAM file" help="A bam
                     file containing all valid Hi-C reads can be created
                     using this option. This bam file could be useful to
                     inspect the distribution of valid Hi-C reads pairs or
                     for other downstream analyses, but is not used by any
                     HiCExplorer tool. Computation will be significantly
-                    longer if this option is set."/>
+                    longer if this option is set." />
 
         <param name='outputFormat' type='select' label="Output file format">
             <option value='h5'>HiCExplorer format</option>
@@ -140,64 +127,63 @@
         </param>
     </inputs>
     <outputs>
-        <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}">
-            <filter>outBam_Boolean</filter>
+        <data name="outfileBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}">
+            <filter>outBam</filter>
         </data>
         <data name="outFileName" from_work_dir="matrix" format="h5" label="${tool.name} MATRIX on ${on_string}">
             <change_format>
                 <when input="outputFormat" value="cool" format="cool" />
             </change_format>
         </data>
-        <data name="qc" format="html" label="${tool.name} QC on ${on_string}"/>
-
+        <data name="qc" format="html" label="${tool.name} QC on ${on_string}" />
         <data name="raw_qc" from_work_dir='raw_qc' format='txt' label="${tool.name} raw QC on ${on_string}" />
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="4">
             <repeat name="samFiles">
-                <param name="samFile" value="small_test_R1_unsorted.sam"/>
+                <param name="samFile" value="small_test_R1_unsorted.sam" dbkey="hg38" />
             </repeat>
             <repeat name="samFiles">
-                <param name="samFile" value="small_test_R2_unsorted.sam"/>
+                <param name="samFile" value="small_test_R2_unsorted.sam" dbkey="hg38" />
+            </repeat>
+            <param name='outputFormat' value='h5' />
+            <repeat name='binSizes'>
+                <param name="binSize" value="5000" />
             </repeat>
-            <conditional name="restrictionCutFileBinSize_conditional">
-                <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/>
-                <repeat name='binSizes'>
-                    <param name="binSize" value="5000"/>
-                </repeat>
-            </conditional>
-            <param name='outputFormat' value='h5'/>
-            <param name='outBam_Boolean' value="True" />
-            <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/>
+            <param name='restrictionCutFile' value='DpnII_10k.bed' />
+            <param name='restrictionSequence' value='GATC' />
+            <param name='danglingSequence' value='GATC' />
+            <param name='outBam' value="True" />
+            <output name="outfileBam" file="small_test_matrix_result_sorted.bam" ftype="bam" />
             <output name="outFileName" ftype="h5">
                 <assert_contents>
-                    <has_h5_keys keys='intervals,matrix'/>
+                    <has_h5_keys keys='intervals,matrix' />
                 </assert_contents>
             </output>
-            <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/>
+            <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2' />
         </test>
-         <test>
+        <test expect_num_outputs="4">
             <repeat name="samFiles">
-                <param name="samFile" value="small_test_R1_unsorted.sam"/>
+                <param name="samFile" value="small_test_R1_unsorted.sam" dbkey="hg38" />
             </repeat>
             <repeat name="samFiles">
-                <param name="samFile" value="small_test_R2_unsorted.sam"/>
+                <param name="samFile" value="small_test_R2_unsorted.sam" dbkey="hg38" />
+            </repeat>
+            <repeat name='binSizes'>
+                <param name="binSize" value="5000" />
             </repeat>
-            <conditional name="restrictionCutFileBinSize_conditional">
-                <param name="restrictionCutFileBinSize_selector" value="optionBinSize"/>
-                <repeat name='binSizes'>
-                    <param name="binSize" value="5000"/>
-                </repeat>
-            </conditional>
-            <param name='outputFormat' value='cool'/>
-            <param name='outBam_Boolean' value="True" />
-            <output name="outBam" file="small_test_matrix_result_sorted.bam" ftype="bam"/>
+            <param name='restrictionCutFile' value='DpnII_10k.bed' />
+            <param name='restrictionSequence' value='GATC' />
+            <param name='danglingSequence' value='GATC' />
+            <param name='outputFormat' value='cool' />
+            <param name='outBam' value="True" />
+            <output name="outfileBam" file="small_test_matrix_result_sorted.bam" ftype="bam" />
             <output name="outFileName" ftype="cool">
                 <assert_contents>
-                    <has_h5_keys keys='bins,chroms,indexes,pixels'/>
+                    <has_h5_keys keys='bins,chroms,indexes,pixels' />
                 </assert_contents>
             </output>
-            <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2'/>
+            <output name="raw_qc" file='raw_qc_report' compare='diff' lines_diff='2' />
         </test>
     </tests>
     <help><![CDATA[
@@ -296,6 +282,6 @@
 | For more information about HiCExplorer please consider our documentation on readthedocs.io_.
 
 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
-]]></help>
+]]>    </help>
     <expand macro="citations" />
 </tool>