--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicAdjustMatrix.xml	Mon Dec 16 15:33:04 2019 -0500
@@ -0,0 +1,114 @@
+<tool id="hicexplorer_hicadjustmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>transform a matrix to obs/exp, pearson and covariance matrices</description>
+    <macros>
+        <token name="@BINARY@">hicAdjustMatrix</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        #set matrix_name = 'matrix_in.' + str($matrix_h5_cooler.ext)
+        #set matrix_file_out = 'matrix_out.' + str($matrix_h5_cooler.ext)
+
+        ln -s '$matrix_h5_cooler' 'matrix_name.$matrix_h5_cooler.ext' &&
+        @BINARY@ --matrix 'matrix_name.$matrix_h5_cooler.ext'
+        --action $action_selector 
+        --outFileName '$matrix_file_out'
+        #if $chromosomeOrRegionFile_conditional.chromosomeOrRegionFile_selector == "optionChromosomes":
+            ## special: --chromosomeOrder is optional, but if given it needs at least one argument
+            #set chroms = '\' \''.join([ str($var.chromosome) for $var in $chromosomeOrRegionFile_conditional.chromosomeOrder ])
+            #if chroms:
+                --chromosomes '$chroms'
+            #end if
+        #end if
+
+        #if $chromosomeOrRegionFile_conditional.chromosomeOrRegionFile_selector == "optionRegionFile":
+                --regions '$chromosomeOrRegionFile_conditional.regions'
+        #end if
+
+        && mv "$matrix_file_out" matrix
+]]>
+    </command>
+    <inputs>
+        <expand macro='matrix_h5_cooler_macro' />
+        <param name="action_selector" type="select" label="Apply action" >
+                <option value="keep" selected="True">keep</option>
+                <option value="remove">remove</option>
+                <option value="mask">mask</option>
+        </param>
+        <conditional name="chromosomeOrRegionFile_conditional">
+            <param name="chromosomeOrRegionFile_selector" type="select" label="List of chromosomes or a BED file containg regions">
+                <option value="optionChromosomes">Chromosomes</option>
+                <option value="optionRegionFile" selected="True">Region BED file</option>
+            </param>
+            <when value="optionChromosomes">
+                 <repeat name="chromosomeOrder" min="0" title="Chromosomes to keep / remove / mask"
+                    help="The selected option will be applied on the selected chromosomes." >
+                    <param name="chromosome" type="text" >
+                        <validator type="empty_field" />
+                    </param>
+                </repeat>
+              
+            </when>
+            <when value="optionRegionFile">
+                <param argument="--regions" type="data" format="bed" optional="true" label="BED file with all regions to be considered."
+                        help="Should contain the regions which should be kept, removed or masked." />
+               
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="outFileName" from_work_dir="matrix" format="h5">
+             <change_format>
+                <when input="matrix_h5_cooler.ext" value="cool" format="cool" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
+            <param name="action_selector" value="keep" />
+            <conditional name="chromosomeOrRegionFile_conditional">
+                <param name="chromosomeOrRegionFile_selector" value='optionChromosomes'/>
+                <repeat name="chromosomeOrder">
+                    <param name="chromosome" value='chrX'/>
+                    <param name="chromosome" value='chr3R'/>
+                </repeat>
+            </conditional>
+
+            <output name="outFileName" ftype="h5">
+                <assert_contents>
+                    <has_h5_keys keys='intervals,matrix'/>
+                </assert_contents>
+            </output>
+        </test>
+
+        <test>
+            <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
+            <param name="action_selector" value="mask" />
+            <conditional name="chromosomeOrRegionFile_conditional">
+                <param name="chromosomeOrRegionFile_selector" value='optionRegionFile'/>
+                <param name="regions" value='regions.bed'/>
+            </conditional>
+
+            <output name="outFileName" ftype="h5">
+                <assert_contents>
+                    <has_h5_keys keys='intervals,matrix,nan_bins'/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Adjust of the Hi-C matrix
+=========================
+
+This tool is able to remove, keep or mask given regions of a Hi-C interaction matrix.
+
+_________________
+
+| 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>