--- a/mergeBed.xml	Sat May 18 23:28:38 2024 +0000
+++ b/mergeBed.xml	Fri Feb 21 21:40:09 2025 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_mergebed" name="bedtools MergeBED" version="@TOOL_VERSION@" profile="@PROFILE@">
+<tool id="bedtools_mergebed" name="bedtools MergeBED" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
     <description>combine overlapping/nearby intervals into a single interval</description>
     <macros>
         <import>macros.xml</import>
@@ -13,10 +13,13 @@
 -d $distance
 $header
 @C_AND_O_ARGUMENT@
+#if $input.ext == "bam"
+    -bed
+#end if
 > '${output}'
     ]]></command>
     <inputs>
-        <param  name="input" argument="-i" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="Sort the following BAM/@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param  name="input" argument="-i" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="Merge the following BAM/@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <param name="strand" type="select" label="Calculation based on strandedness?">
             <option value="" selected="true">Overlaps on either strand</option>
             <option value="-s">Force strandedness. That is, only merge features that are the same strand (-s)</option>
@@ -25,7 +28,7 @@
         </param>
         <param name="distance" argument="-d" type="integer" value="0"
             label="Maximum distance between features allowed for features to be merged"
-            help="That is, overlapping and/or book-ended features are merged"/>
+            help="Default 0: overlapping and/or book-ended features are merged. Note: negative values enforce the number of b.p. required for overlap."/>
         <expand macro="print_header" />
         <expand macro="c_and_o_argument">
             <param name="col" argument="-c" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" />
@@ -38,20 +41,48 @@
         <test>
             <param name="input" value="mergedBed1.bed" ftype="bed" />
             <output name="output" file="mergedBed_result1.bed" ftype="bed" />
+            <assert_command>
+                <not_has_text text="-s "/>
+                <not_has_text text="-S "/>
+                <has_text text="-d 0"/>
+                <not_has_text text="-c "/>
+                <not_has_text text="-o "/>
+            </assert_command>
         </test>
         <test>
             <param name="input" value="mergedBed2.bed" ftype="bed" />
             <param name="strand" value="-s" />
             <output name="output" file="mergedBed_result2.bed" ftype="bed" />
+            <assert_command>
+                <has_text text="-s "/>
+                <not_has_text text="-S "/>
+                <has_text text="-d 0"/>
+                <not_has_text text="-c "/>
+                <not_has_text text="-o "/>
+            </assert_command>
         </test>
         <test>
             <param name="input" value="mergedBed3.bed" ftype="bed" />
             <output name="output" file="mergedBed_result3.bed" ftype="bed" />
+            <assert_command>
+                <not_has_text text="-s "/>
+                <not_has_text text="-S "/>
+                <has_text text="-d 0"/>
+                <not_has_text text="-c "/>
+                <not_has_text text="-o "/>
+            </assert_command>
         </test>
         <test>
             <param name="input" value="mergedBed4.bed" ftype="bed" />
             <param name="distance" value="1000" />
             <output name="output" file="mergedBed_result4.bed" ftype="bed" />
+            <assert_command>
+                <not_has_text text="-s "/>
+                <not_has_text text="-S "/>
+                <has_text text="-d 1000"/>
+                <not_has_text text="-c "/>
+                <not_has_text text="-o "/>
+            </assert_command>
         </test>
         <test>
             <param name="input" value="mergedBed4.bed" ftype="bed" />
@@ -61,6 +92,13 @@
                 <param name="operation" value="count"/>
             </repeat>
             <output name="output" file="mergedBed_result5.bed" ftype="bed" />
+            <assert_command>
+                <not_has_text text="-s "/>
+                <not_has_text text="-S "/>
+                <has_text text="-d 1000"/>
+                <has_text text="-c 1"/>
+                <has_text text="-o count"/>
+            </assert_command>
         </test>
     </tests>
     <help><![CDATA[