--- a/makeWindowsBed.xml	Sat May 18 23:28:38 2024 +0000
+++ b/makeWindowsBed.xml	Fri Feb 21 21:40:09 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_makewindowsbed" name="bedtools MakeWindowsBed" version="@TOOL_VERSION@" profile="@PROFILE@">
+<tool id="bedtools_makewindowsbed" name="bedtools MakeWindowsBed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>make interval windows across a genome</description>
     <macros>
         <import>macros.xml</import>
@@ -15,8 +15,8 @@
 #end if
 #if $action.action_select == 'windowsize':
     -w $action.windowsize
-    #if $action.step_size.step_size_select == 'yes':
-        -s $action.step_size.step_size
+    #if $action.step_size != '':
+        -s $action.step_size
     #end if
 #else:
     -n $action.number
@@ -46,18 +46,7 @@
                 <param name="windowsize" argument="-w" type="integer" value="1"
                     label="Divide each input interval (either a chromosome or a BED interval) to fixed-sized windows"
                     help="i.e. same number of nucleotide in each window" />
-                 <conditional name="step_size">
-                    <param name="step_size_select" type="select"
-                        label="Specify Step size? i.e. how many base pairs to step before creating a new window"
-                        help="Used to create 'sliding' windows. Defaults to window size (non-sliding windows).">
-                        <option value="yes">Yes</option>
-                        <option value="no" selected="true">No</option>
-                    </param>
-                    <when value="yes">
-                        <param name="step_size" argument="-s" type="integer" value="100" label="Specify it" />
-                    </when>
-                    <when value="no" />
-                 </conditional>
+                <param name="step_size" argument="-s" type="integer" value="" optional="true" label="Step size" help="How many base pairs to step before creating a new window. Used to create 'sliding' windows. Defaults to window size (non-sliding windows)."/>
             </when>
             <when value="number">
                 <param name="number" argument="-n" type="integer" value="1"
@@ -77,36 +66,35 @@
     </outputs>
     <tests>
         <test>
-            <param name="type_select" value="genome" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="mm9_chr1.len" ftype="tabular" />
-            <param name="action_select" value="windowsize" />
-            <param name="windowsize" value="1000000" />
+            <param name="type|type_select" value="genome" />
+            <param name="type|genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="type|genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular" />
+            <param name="action|action_select" value="windowsize" />
+            <param name="action|windowsize" value="1000000" />
             <output name="output" file="makeWindowBed_result1.bed" ftype="bed" />
         </test>
         <test>
-            <param name="type_select" value="genome" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="mm9_chr1.len" ftype="tabular" />
-            <param name="action_select" value="windowsize" />
-            <param name="windowsize" value="1000000" />
-            <param name="step_size_select" value="yes" />
-            <param name="step_size" value="50000" />
+            <param name="type|type_select" value="genome" />
+            <param name="type|genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="type|genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular" />
+            <param name="action|action_select" value="windowsize" />
+            <param name="action|windowsize" value="1000000" />
+            <param name="action|step_size" value="50000" />
             <output name="output" file="makeWindowBed_result2.bed" ftype="bed" />
         </test>
         <test>
-            <param name="type_select" value="genome" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="mm9_chr1.len" ftype="tabular" />
-            <param name="action_select" value="number" />
-            <param name="number" value="100" />
+            <param name="type|type_select" value="genome" />
+            <param name="type|genome_file_opts|genome_file_opts_selector" value="hist" />
+            <param name="type|genome_file_opts|genome" value="mm9_chr1.len" ftype="tabular" />
+            <param name="action|action_select" value="number" />
+            <param name="action|number" value="100" />
             <output name="output" file="makeWindowBed_result3.bed" ftype="bed" />
         </test>
         <test>
-            <param name="type_select" value="bed" />
-            <param name="input" value="makeWindowBed1.bed" ftype="bed" />
-            <param name="action_select" value="number" />
-            <param name="number" value="15" />
+            <param name="type|type_select" value="bed" />
+            <param name="type|input" value="makeWindowBed1.bed" ftype="bed" />
+            <param name="action|action_select" value="number" />
+            <param name="action|number" value="15" />
             <output name="output" file="makeWindowBed_result4.bed" ftype="bed" />
         </test>
     </tests>