--- a/hicNormalize.xml	Tue Jan 10 17:50:20 2023 +0000
+++ b/hicNormalize.xml	Mon Jul 01 19:06:47 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicnormalize" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+<tool id="hicexplorer_hicnormalize" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>normalizes a matrix to norm range or smallest read count</description>
     <macros>
         <token name="@BINARY@">hicNormalize</token>
@@ -28,23 +28,23 @@
 ]]>
     </command>
     <inputs>
-        <expand macro='matrix_h5_cooler_multiple_macro' />
+        <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 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'>
+            <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" />
+        <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">
+        <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" />
@@ -54,7 +54,7 @@
     <tests>
         <test>
             <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool" />
-            <param name='normalize' value='norm_range' />
+            <param name="normalize" value="norm_range" />
             <output name="normalize_matrix">
                 <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool">
                     <assert_contents>
@@ -65,7 +65,7 @@
         </test>
         <test>
             <param name="matrix_h5_cooler_multiple" value="small_test_matrix.cool,small_test_matrix.cool" />
-            <param name='normalize' value='smallest' />
+            <param name="normalize" value="smallest" />
             <output name="normalize_matrix">
                 <discovered_dataset designation="0_norm_small_test_matrix" ftype="cool">
                     <assert_contents>
@@ -81,7 +81,7 @@
         </test>
         <test>
             <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5" />
-            <param name='normalize' value='smallest' />
+            <param name="normalize" value="smallest" />
             <output name="normalize_matrix">
                 <discovered_dataset designation="0_norm_small_test_matrix" ftype="h5">
                     <assert_contents>
@@ -115,7 +115,7 @@
 | 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/science.1181369
+.. _`Lieberman-Aiden et al. (2009)`: https://pubmed.ncbi.nlm.nih.gov/19815776/
 ]]>    </help>
     <expand macro="citations" />
 </tool>