# HG changeset patch
# User iuc
# Date 1676929788 0
# Node ID 589e7e57fd6dc207585f200f92bd3b5910f60ba5
# Parent  07e8b80f278c356cddee2622b1075f36a2da647e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 03a91f6c42c75dc36d09505c2e6a2236178e4695

diff -r 07e8b80f278c -r 589e7e57fd6d mergeBed.xml
--- a/mergeBed.xml	Fri Apr 01 19:02:51 2022 +0000
+++ b/mergeBed.xml	Mon Feb 20 21:49:48 2023 +0000
@@ -41,12 +41,11 @@
         </test>
         <test>
             <param name="input" value="mergedBed2.bed" ftype="bed" />
-            <param name="strandedness" value="-s" />
+            <param name="strand" value="-s" />
             <output name="output" file="mergedBed_result2.bed" ftype="bed" />
         </test>
         <test>
             <param name="input" value="mergedBed3.bed" ftype="bed" />
-            <param name="report_number" value="-n" />
             <output name="output" file="mergedBed_result3.bed" ftype="bed" />
         </test>
         <test>
diff -r 07e8b80f278c -r 589e7e57fd6d sortBed.xml
--- a/sortBed.xml	Fri Apr 01 19:02:51 2022 +0000
+++ b/sortBed.xml	Mon Feb 20 21:49:48 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_sortbed" name="bedtools SortBED" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
+<tool id="bedtools_sortbed" name="bedtools SortBED" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
     <description>order the intervals</description>
     <macros>
         <import>macros.xml</import>
@@ -25,7 +25,7 @@
             <option value="-chrThenScoreA">chromosome, then by score (asc).</option>
             <option value="-chrThenScoreD">chromosome, then by score (desc).</option>
         </param>
-        <expand macro="input_conditional_genome_file" help="Sort according to the chromosomes declared in a genome file" />
+        <expand macro="input_conditional_genome_file" optional="true" help="Sort according to the chromosomes declared in a genome file" />
     </inputs>
     <outputs>
         <data name="output" format_source="input" metadata_source="input" label="SortBed on ${input.name}"/>
diff -r 07e8b80f278c -r 589e7e57fd6d test-data/mergedBed_result2.bed
--- a/test-data/mergedBed_result2.bed	Fri Apr 01 19:02:51 2022 +0000
+++ b/test-data/mergedBed_result2.bed	Mon Feb 20 21:49:48 2023 +0000
@@ -1,2 +1,3 @@
-chr1	100	500
+chr1	100	250
+chr1	250	500
 chr1	501	1000
diff -r 07e8b80f278c -r 589e7e57fd6d test-data/sortBed_result2.bed
--- a/test-data/sortBed_result2.bed	Fri Apr 01 19:02:51 2022 +0000
+++ b/test-data/sortBed_result2.bed	Mon Feb 20 21:49:48 2023 +0000
@@ -1,3 +1,3 @@
 chr1	800	1000
+chr10	80	180
 chr2	1	10
-chr10	80	180