diff intersectBed.xml @ 43:07e8b80f278c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"

--- a/intersectBed.xml	Wed Jan 12 19:22:14 2022 +0000
+++ b/intersectBed.xml	Fri Apr 01 19:02:51 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@" profile="@PROFILE@">
+<tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>find overlapping intervals in various ways</description>
     <macros>
         <import>macros.xml</import>
@@ -51,6 +51,7 @@
 $header
 $modes
 @SORTED@
+@GENOME_FILE@
 $bed
 $count
 > '${output}'
@@ -117,6 +118,7 @@
             label="When using BAM input, write output as BED instead of BAM." />
         <!-- -sorted -g  -->
         <expand macro="sorted" />
+        <expand macro="input_conditional_genome_file" optional="true" help="Only applies when used with -sorted option."/>
         <expand macro="print_header" />
     </inputs>
     <outputs>
@@ -151,7 +153,7 @@
                 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
             </conditional>
             <param name="overlap_mode" value="-wa,-wb" />
-            <param name="sorted" value="-sorted" />
+            <param name="sorted" value="true" />
             <output name="output" file="intersect-multiple-wa-wb.bed" ftype="bed" />
         </test>
         <test>
@@ -163,7 +165,7 @@
                 <param name="names" value="yes" />
             </conditional>
             <param name="overlap_mode" value="-wa,-wb" />
-            <param name="sorted" value="-sorted" />
+            <param name="sorted" value="true" />
             <output name="output" file="intersect-multiple-wa-wb-wnames.bed" ftype="bed" />
         </test>
         <test>
@@ -173,7 +175,7 @@
                 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
             </conditional>
             <param name="invert" value="-v" />
-            <param name="sorted" value="-sorted" />
+            <param name="sorted" value="true" />
             <output name="output" file="intersect-multiple-invert.bed" ftype="bed" />
         </test>
         <test>
@@ -187,7 +189,7 @@
                 <param name="fraction_select" value="specify"/>
                 <param name="overlap" value="1.0" />
             </conditional>
-            <param name="sorted" value="-sorted" />
+            <param name="sorted" value="true" />
             <output name="output" file="intersect-multiple-fracA.bed" ftype="bed" />
         </test>
         <test>