--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicValidateLocations.xml	Mon Dec 16 14:30:02 2019 -0500
@@ -0,0 +1,74 @@
+<tool id="hicexplorer_hicvalidatelocations" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>validate detected loops with protein peaks.</description>
+    <macros>
+        <token name="@BINARY@">hicValidateLocations</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+   
+        @BINARY@
+            --data '$data'
+            --protein '$protein'
+            --method loops
+            --resolution '$resolution'
+            $addChrPrefixLoops
+            $addChrPrefixProtein
+            --outFileName outfile
+    ]]></command>
+    <inputs>
+        <param argument="--data" type="data" format='bed'
+                        label="Loop file"
+                        help="The loop file from hicDetectLoops. To use files from other sources, '
+                                'please follow \'chr start end chr start end\' format." />
+        <param argument="--protein" type="data" format='bed'
+                        label="Loop file"
+                        help="The loop file from hicDetectLoops. To use files from other sources, '
+                                'please follow \'chr start end chr start end\' format." />
+        <param argument="--resolution" type="integer" value=""
+                label="Used resolution"
+                help='The to be binned resolution.'/>    
+
+        <param name='addChrPrefixLoops' type='boolean' truevalue='--addChrPrefixLoops'  falsevalue="" checked="false" label="Add chr prefix to loops."
+                    help="Adding a \'chr\'-prefix to chromosome name of the loops."/>
+        
+        <param name='addChrPrefixProtein' type='boolean' truevalue='--addChrPrefixLoops'  falsevalue="" checked="false" label="Add chr prefix to protein."
+                    help="Adding a \'chr\'-prefix to chromosome name of the protein."/>
+   
+    </inputs>
+    <outputs>
+        <data name="statistic" from_work_dir="outfile_statistics" format="bed" label="${tool.name} on [${on_string}]: Statistic"/>
+        <data name="mergedLoops" from_work_dir="outfile_matched_locations" format="bed" label="${tool.name} on [${on_string}]: Matched locations"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="data" ftype='bed' value="hicValidateLocations/loops_1.bedgraph"/>
+            <param name="protein" ftype='bed' value="hicValidateLocations/GSM935376_hg19_Gm12878_Smc3.narrowPeak"/>
+            <param name="resolution" value="10000"/>
+            <param name="addChrPrefixLoops" value="True"/>
+            <output name="statistic" file="hicValidateLocations/overlap_smc3_statistics" ftype="bed" compare="sim_size" delta='40000'/>
+            <output name="mergedLoops" file="hicValidateLocations/overlap_smc3_matched_locations" ftype="bed" compare="sim_size" delta='40000'/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Validate locations
+==================
+
+This script overlaps the loop locations with protein locations to determine the accuracy of the loop detection.
+Loops need to have format as follows:
+
+`chr start end chr start end`
+
+The protein peaks need to be in narrowPeaks or broadPeak format.
+
+A protein match is successfull if at the bin of the x and y location a protein peak is overlapped.
+A bin is assumed to have a protein if one or more protein peaks falling within the bin region.
+The value of the protein is not considered, only match or non-match.
+
+For more information about HiCExplorer please consider our documentation on readthedocs.io_
+
+.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
+]]></help>
+    <expand macro="citations" />
+</tool>