diff jaccardBed.xml @ 46:64e2edfe7a2c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3e7bf5ae62de3520635d75e3825701960b9722e4

--- a/jaccardBed.xml	Thu Mar 02 08:52:08 2023 +0000
+++ b/jaccardBed.xml	Sat May 18 23:28:38 2024 +0000
@@ -3,9 +3,9 @@
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="bio_tools" />
-    <expand macro="requirements" />
-    <expand macro="stdio" />
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
     <command><![CDATA[
 bedtools jaccard
 $strand
@@ -22,29 +22,33 @@
     <inputs>
         <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
-        <expand macro="overlap" />
+        <expand macro="overlap"/>
         <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/>
-        <expand macro="reciprocal" />
-        <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
-            label="Force strandedness"
-            help="That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand." />
-        <expand macro="strand2" />
-        <expand macro="split" />
+        <expand macro="reciprocal"/>
+        <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Force strandedness" help="That is, only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand."/>
+        <expand macro="split"/>
     </inputs>
     <outputs>
-        <data name="output" format_source="inputA" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}" />
+        <data name="output" format_source="inputA" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}"/>
     </outputs>
     <tests>
         <test>
-            <param name="inputA" value="jaccardBed1.bed" ftype="bed" />
-            <param name="inputB" value="jaccardBed2.bed" ftype="bed" />
-            <output name="output" file="jaccardBed_result1.bed" ftype="bed" />
+            <param name="inputA" value="jaccardBed1.bed" ftype="bed"/>
+            <param name="inputB" value="jaccardBed2.bed" ftype="bed"/>
+            <output name="output" file="jaccardBed_result1.bed" ftype="bed"/>
         </test>
         <test>
-            <param name="inputA" value="jaccardBed1.bed" ftype="bed" />
-            <param name="inputB" value="jaccardBed2.bed" ftype="bed" />
-            <param name="overlap" value="0.1" />
-            <output name="output" file="jaccardBed_result2.bed" ftype="bed" />
+            <param name="inputA" value="jaccardBed1.bed" ftype="bed"/>
+            <param name="inputB" value="jaccardBed2.bed" ftype="bed"/>
+            <param name="overlap" value="0.1"/>
+            <output name="output" file="jaccardBed_result2.bed" ftype="bed"/>
+        </test>
+        <test>
+            <param name="inputA" value="jaccardBed1.bed" ftype="bed"/>
+            <param name="inputB" value="jaccardBed2.bed" ftype="bed"/>
+            <param name="overlap" value="0.1"/>
+            <param name="strand" value="true"/>
+            <output name="output" file="jaccardBed_strand_result2.bed" ftype="bed"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -61,5 +65,5 @@
 
 @REFERENCES@
     ]]></help>
-    <expand macro="citations" />
+    <expand macro="citations"/>
 </tool>