--- a/hicCorrectMatrix.xml	Fri Dec 11 21:01:31 2020 +0000
+++ b/hicCorrectMatrix.xml	Tue Mar 16 15:41:08 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hiccorrectmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_hiccorrectmatrix" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>run a Hi-C matrix correction algorithm</description>
     <macros>
         <token name="@BINARY@">hicCorrectMatrix</token>
@@ -68,8 +68,7 @@
             </param>
             <when value="diagnostic_plot">
                 <expand macro="xMax" />
-                <param argument="--perchr" name="perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false"
-                            label="Compute statistics for each chromosome separately" />
+                <param argument="--perchr" name="perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Compute statistics for each chromosome separately" />
             </when>
             <when value="correct">
                 <conditional name='correctionMethod'>
@@ -79,28 +78,19 @@
                     </param>
 
                     <when value='ice'>
-                        <param argument="--iterNum" name="iterNum" type="integer" optional="true" value="500"
-                            label="Number of iterations" />
+                        <param argument="--iterNum" name="iterNum" type="integer" optional="true" value="500" label="Number of iterations" />
 
-                        <param argument="--inflationCutoff" name="inflationCutoff" type="float" optional="true"
-                            label="Inflation cutoff" value=""
-                            help="Value corresponding to the maximum number of times a bin can be scaled up during the iterative correction.
-                            For example, a inflationCutoff of 3 will filter out all bins that were expanded 3 times or more during the iterative correction."/>
+                        <param argument="--inflationCutoff" name="inflationCutoff" type="float" optional="true" label="Inflation cutoff" value="" help="Value corresponding to the maximum number of times a bin can be scaled up during the iterative correction.
+                            For example, a inflationCutoff of 3 will filter out all bins that were expanded 3 times or more during the iterative correction." />
+
+                        <param argument="--transCutoff" name="transCutoff" type="float" optional="true" label="Trans region cutoff" value="" help="Clip high counts in the top -transcut trans regions (i.e. between chromosomes). A usual value is 0.05." />
 
-                        <param argument="--transCutoff" name="transCutoff" type="float" optional="true"
-                            label="Trans region cutoff" value=""
-                            help="Clip high counts in the top -transcut trans regions (i.e. between chromosomes). A usual value is 0.05."/>
+                        <param argument="--sequencedCountCutoff" name="sequencedCountCutoff" optional="true" type="float" label="Sequenced count cutoff" help="Each bin receives a value indicating the fraction that is covered by reads.
+                                A cutoff of 0.5 will discard all those bins that have less than half of the bin covered." />
 
-                        <param argument="--sequencedCountCutoff" name="sequencedCountCutoff" optional="true" type="float"
-                            label="Sequenced count cutoff"
-                            help="Each bin receives a value indicating the fraction that is covered by reads.
-                                A cutoff of 0.5 will discard all those bins that have less than half of the bin covered."/>
+                        <param argument="--skipDiagonal" name="skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" checked="false" label="Skip diagonal counts" />
 
-                        <param argument="--skipDiagonal" name="skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" checked="false"
-                            label="Skip diagonal counts"/>
-
-                        <param argument="--perchr" name="perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false"
-                            label="Normalize each chromosome separately" />
+                        <param argument="--perchr" name="perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Normalize each chromosome separately" />
                         <expand macro="filterThreshold" />
                     </when>
                     <when value='kr'>
@@ -109,8 +99,7 @@
             </when>
         </conditional>
 
-        <repeat name="chromosomes" min="0"
-            title="Include chromosomes" help="List of chromosomes to be included in the iterative correction.
+        <repeat name="chromosomes" min="0" title="Include chromosomes" help="List of chromosomes to be included in the iterative correction.
                     The order of the given chromosomes will be kept for the resulting corrected matrix">
             <param name="chromosome" type="text" value="" label='chromosome (one per field)'>
                 <validator type="empty_field" />
@@ -121,90 +110,82 @@
     <outputs>
         <data name="outFileName" from_work_dir="matrix" format="cool">
             <change_format>
-                <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5"/>
+                <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5" />
             </change_format>
             <filter>mode['mode_selector'] == "correct"</filter>
-
         </data>
-
-
         <data name="diagnostic_plot" from_work_dir="diagnostic_plot.png" format="png">
             <filter>mode['mode_selector'] == "diagnostic_plot"</filter>
         </data>
     </outputs>
     <tests>
         <test>
-            <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
-
-            <param name="mode_selector" value="correct"/>
-            <param name='correctionMethod_selector' value='ice'/>
+            <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
+            <param name="mode_selector" value="correct" />
+            <param name='correctionMethod_selector' value='ice' />
             <repeat name="chromosomes">
-                <param name="chromosome" value="chrUextra"/>
+                <param name="chromosome" value="chrUextra" />
             </repeat>
             <repeat name="chromosomes">
-                <param name="chromosome" value="chr3LHet"/>
+                <param name="chromosome" value="chr3LHet" />
             </repeat>
             <param name='filterThreshold_low' value='-2.0' />
             <param name='filterThreshold_large' value='4' />
             <output name="outFileName" ftype="h5">
                 <assert_contents>
-                    <has_h5_keys keys='correction_factors,intervals,matrix,nan_bins'/>
+                    <has_h5_keys keys='correction_factors,intervals,matrix,nan_bins' />
                 </assert_contents>
             </output>
         </test>
         <test>
-            <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
-
-            <param name="mode_selector" value="correct"/>
-            <param name='correctionMethod_selector' value='kr'/>
-
+            <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
+            <param name="mode_selector" value="correct" />
+            <param name='correctionMethod_selector' value='kr' />
             <output name="outFileName" ftype="h5">
                 <assert_contents>
-                    <has_h5_keys keys='correction_factors,intervals,matrix'/>
+                    <has_h5_keys keys='correction_factors,intervals,matrix' />
                 </assert_contents>
             </output>
         </test>
         <test>
-            <param name="matrix_h5_cooler" value="small_test_matrix.cool"/>
-
-            <param name="mode_selector" value="correct"/>
-            <param name='correctionMethod_selector' value='kr'/>
-
+            <param name="matrix_h5_cooler" value="small_test_matrix.cool" />
+            <param name="mode_selector" value="correct" />
+            <param name='correctionMethod_selector' value='kr' />
             <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>
         </test>
         <test>
-            <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
+            <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
 
-            <param name="mode_selector" value="correct"/>
-            <param name='correctionMethod_selector' value='ice'/>
+            <param name="mode_selector" value="correct" />
+            <param name='correctionMethod_selector' value='ice' />
             <repeat name="chromosomes">
-                <param name="chromosome" value="chrUextra"/>
+                <param name="chromosome" value="chrUextra" />
             </repeat>
             <repeat name="chromosomes">
-                <param name="chromosome" value="chr3LHet"/>
+                <param name="chromosome" value="chr3LHet" />
             </repeat>
             <param name='filterThreshold_low' value='-2.0' />
             <param name='filterThreshold_large' value='4' />
             <output name="outFileName" ftype="h5">
                 <assert_contents>
-                    <has_h5_keys keys='correction_factors,intervals,matrix,nan_bins'/>
+                    <has_h5_keys keys='correction_factors,intervals,matrix,nan_bins' />
                 </assert_contents>
             </output>
         </test>
         <test>
-            <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
-            <param name="mode_selector" value="diagnostic_plot"/>
+            <param name="matrix_h5_cooler" value="small_test_matrix.h5" />
+            <param name="mode_selector" value="diagnostic_plot" />
             <repeat name="chromosomes">
-                <param name="chromosome" value="chrUextra"/>
+                <param name="chromosome" value="chrUextra" />
             </repeat>
             <repeat name="chromosomes">
-                <param name="chromosome" value="chr3LHet"/>
+                <param name="chromosome" value="chr3LHet" />
             </repeat>
-            <output name="diagnostic_plot" file="hicCorrectMatrix/diagnostic_plot.png" ftype="png" compare="sim_size"/>
+            <output name="diagnostic_plot" file="hicCorrectMatrix/diagnostic_plot.png" ftype="png" compare="sim_size" />
         </test>
     </tests>
     <help><![CDATA[
@@ -275,6 +256,6 @@
 
 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
 .. _`Imakaev et al. (2012)`: https://doi.org/10.1038/nmeth.2148
-]]></help>
+]]>    </help>
     <expand macro="citations" />
 </tool>