# HG changeset patch
# User iuc
# Date 1673377349 0
# Node ID 2a24ce221cd73b143e7cc1cb0c6baa3535a240ac
# Parent  3e598b8e72e7e6a09c314e34de073c38ab6a64c1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa140a9f660eab2459e21b0b637b129d7de24c02

diff -r 3e598b8e72e7 -r 2a24ce221cd7 hicConvertFormat.xml
--- a/hicConvertFormat.xml	Tue Mar 16 15:38:11 2021 +0000
+++ b/hicConvertFormat.xml	Tue Jan 10 19:02:29 2023 +0000
@@ -88,16 +88,8 @@
             --outputFormat $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector
             --outFileName 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector'
 
-            #if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'ginteractions':
-                && mv 'matrix.${outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector}.tsv' matrix_out
-            #else:
-                && mv 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector' matrix_out
-            #end if
-        #end if
-
-
         ### Set up links to matrices to have correct ending
-        #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix':
+        #else if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix':
             #if $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.resolutionOrManyToOne_selector == 'resolution_option':
                 #set xml_path = $outputSingleMultiple_conditional.resolutionOrManyToOne_conditional.inputFormat_conditional
                 #if $xml_path.inputFormat_selector == 'optionCool':
@@ -206,6 +198,17 @@
                 --matrices $m
             #end if
             --outFileName matrix.mcool
+        #end if
+        $storeAppliedCorrection
+        $enforceInteger
+
+        #if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'singleMatrix':
+            #if $outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector == 'ginteractions':
+                && mv 'matrix.${outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector}.tsv' matrix_out
+            #else:
+                && mv 'matrix.$outputSingleMultiple_conditional.outputFormat_conditional.outputFormat_selector' matrix_out
+            #end if
+        #else if $outputSingleMultiple_conditional.outputSingleMultiple_selector == 'multipleMatrix':
             && mv matrix.mcool matrix_out
         #end if
 ]]>
@@ -237,10 +240,10 @@
                         <expand macro='convertFormat_multiple_macro' />
                     </when>
                 </conditional>
-                <param name='storeAppliedCorrection' type="boolean" truevalue="yes" falsevalue="" label='Store applied correction factors in column count' />
-                <param name='enforceInteger' type="boolean" truevalue="yes" falsevalue="" label='Enforce integer for count column' />
             </when>
         </conditional>
+        <param name='storeAppliedCorrection' type="boolean" truevalue="--store_applied_correction" falsevalue="" label="Store applied correction factors in column count" help="Option only for cool input files" />
+        <param name='enforceInteger' type="boolean" truevalue="--enforce_integer" falsevalue="" label="Enforce integer for count column" help="Option only for cool input files" />
     </inputs>
     <outputs>
         <data name='output_converted_matrix' from_work_dir='matrix_out' format='cool' label='Converted matrix'>
diff -r 3e598b8e72e7 -r 2a24ce221cd7 macros.xml
--- a/macros.xml	Tue Mar 16 15:38:11 2021 +0000
+++ b/macros.xml	Tue Jan 10 19:02:29 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." />