--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicNormalize.xml	Thu Feb 06 01:03:09 2020 +0000
@@ -0,0 +1,110 @@
+<tool id="hicexplorer_hicnormalize" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>normalizes a matrix to norm range or smallest read count</description>
+    <macros>
+        <token name="@BINARY@">hicNormalize</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        #import re
+
+        mkdir output &&
+        #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
+            ln -s '$m' '${counter}_matrix.$m.ext' &&
+        #end for
+        #set $m = ' '.join([ '\'%s_matrix.%s\'' % ($counter, $matrix.ext) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
+        #set $m_out = ' '.join([ "'output/%s_norm_%s'" % ($counter, @ESCAPE_IDENTIFIER_MATRIX@) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
+
+        @BINARY@ --matrices $m
+        #if $normalize_conditional.normalize == 'multiplicative':
+            --multiplicativeValue $normalize_conditional.multiplicativeValue
+        #end if
+        --normalize $normalize_conditional.normalize
+        #if $zero_threshold_value:
+            --setToZeroThreshold $zero_threshold_value
+        #end if
+
+        --outFileName $m_out
+]]>
+    </command>
+    <inputs>
+        <expand macro='matrix_h5_cooler_multiple_macro'/>
+        <conditional name="normalize_conditional">
+            <param name='normalize' type='select' label='Normalize matrices'>
+                <option value='norm_range'>0 to 1 range</option>
+                <option value='smallest'>Smallest read count</option>
+                <option value='multiplicative'>Multiply by value</option>
+            </param>
+            <when value='norm_range'/>
+            <when value='smallest'/>
+            <when value='multiplicative'>
+                <param name="multiplicativeValue" type="float" value="1.0" label="Multiplicative value"/>
+            </when>
+        </conditional>
+        <param name="zero_threshold_value" type="float" value="1.0" optional='True' label="Set values below this threshold to zero"/>
+    </inputs>
+    <outputs>
+        <data format='cool' name="normalize_matrix">
+            <discover_datasets pattern="__name_and_ext__" directory="output"  visible="true"/>
+            <change_format>
+                <when input_dataset="matrix_h5_cooler_multiple" attribute="ext" value="h5" format="h5"/>
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool"/>
+            <param name='normalize' value='norm_range'/>
+            <output name="normalize_matrix">
+                <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool">
+                    <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents>
+                </discovered_dataset>
+            </output>
+        </test>
+        <test>
+            <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool,small_test_matrix.cool"/>
+            <param name='normalize' value='smallest'/>
+            <output name="normalize_matrix">
+                <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool">
+                    <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents>
+                </discovered_dataset>
+                <discovered_dataset designation="1_norm_small_test_matrix" ftype="cool">
+                    <assert_contents><has_h5_keys keys="bins,chroms,indexes,pixels"/></assert_contents>
+                </discovered_dataset>
+            </output>
+        </test>
+        <test>
+            <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5"/>
+            <param name='normalize' value='smallest'/>
+            <output name="normalize_matrix">
+                <discovered_dataset designation="0_norm_small_test_matrix" ftype="h5">
+                    <assert_contents><has_h5_keys keys="intervals,matrix"/></assert_contents>
+                </discovered_dataset>
+                <discovered_dataset designation="1_norm_small_test_matrix" ftype="h5">
+                    <assert_contents><has_h5_keys keys="intervals,matrix"/></assert_contents>
+                </discovered_dataset>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Normalization of matrices
+=========================
+
+**hicNormalize** normalizes either each matrix to a 0 - 1 value range, to the smallest read coverage or with a user given factor.
+
+_________________
+
+Output
+------
+
+The normalized matrices.
+
+_________________
+
+| For more information about HiCExplorer please consider our documentation on readthedocs.io_
+
+.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
+.. _`Lieberman-Aiden et al. (2009)`: https://doi.org/10.1126%2Fscience.1181369
+]]></help>
+    <expand macro="citations" />
+</tool>