--- a/hicCorrectMatrix.xml	Tue Mar 16 15:41:08 2021 +0000
+++ b/hicCorrectMatrix.xml	Tue Jan 10 18:37:39 2023 +0000
@@ -6,7 +6,7 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
+        cp '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
 
         @BINARY@
             $mode.mode_selector
@@ -55,7 +55,7 @@
                 $mode.perchr
             #end if
         #if $mode.mode_selector == 'correct':
-            && mv matrix.$matrix_h5_cooler.ext matrix
+            && mv matrix.$matrix_h5_cooler.ext '$outFileName'
         #end if
 ]]>
     </command>
@@ -68,7 +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" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Compute statistics for each chromosome separately" />
             </when>
             <when value="correct">
                 <conditional name='correctionMethod'>
@@ -78,19 +78,19 @@
                     </param>
 
                     <when value='ice'>
-                        <param argument="--iterNum" name="iterNum" type="integer" optional="true" value="500" label="Number of iterations" />
+                        <param argument="--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.
+                        <param argument="--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" 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.
+                        <param argument="--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" 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" type="boolean" truevalue="--perchr" falsevalue="" checked="false" label="Normalize each chromosome separately" />
                         <expand macro="filterThreshold" />
                     </when>
                     <when value='kr'>
@@ -108,13 +108,13 @@
 
     </inputs>
     <outputs>
-        <data name="outFileName" from_work_dir="matrix" format="cool">
+        <data name="outFileName" format="cool">
             <change_format>
                 <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">
+        <data name="diagnostic_plot" from_work_dir="diagnostic_plot.png" format="png" label="${tool.name} on ${on_string}: Diagnostic plot">
             <filter>mode['mode_selector'] == "diagnostic_plot"</filter>
         </data>
     </outputs>

--- a/macros.xml	Tue Mar 16 15:41:08 2021 +0000
+++ b/macros.xml	Tue Jan 10 18:37:39 2023 +0000
@@ -1,7 +1,7 @@
 <macros>
     <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token>
     <token name="@TOOL_VERSION@">3.6</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@USE_RANGE@">
         #if $use_range.select_use_range == "yes_use_range":
             --range $use_range.range_min:$use_range.range_max
@@ -333,7 +333,7 @@
         <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)" />
     </xml>
     <xml name="xMax">
-        <param argument="--xMax" name="xMax" type="integer" optional="true" value="" label="Max value for the x-axis in counts per bin" />
+        <param argument="--xMax" type="integer" optional="true" value="" label="Max value for the x-axis in counts per bin" />
     </xml>
     <xml name="filterThreshold">
         <param argument="--filterThreshold" name="filterThreshold_low" type="float" value="-1.5" label="Remove bins of low coverage" help="e.g. -1.5; Both Thresholds needs to be set to take effect." />