diff mapBed.xml @ 43:07e8b80f278c draft

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

--- a/mapBed.xml	Wed Jan 12 19:22:14 2022 +0000
+++ b/mapBed.xml	Fri Apr 01 19:02:51 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="bedtools_map" name="bedtools MapBed" version="@TOOL_VERSION@.2" profile="@PROFILE@">
+<tool id="bedtools_map" name="bedtools MapBed" version="@TOOL_VERSION@.3" profile="@PROFILE@">
     <description>apply a function to a column for each overlapping interval</description>
     <macros>
         <import>macros.xml</import>
@@ -19,7 +19,7 @@
 $reciprocal
 $split
 $header
-@GENOME_FILE_MAPBED@
+@GENOME_FILE@
 > '${output}'
     ]]></command>
     <inputs>
@@ -36,7 +36,7 @@
         </expand>
         <expand macro="split" />
         <expand macro="print_header" />
-        <expand macro="input_optional_genome_file" />
+        <expand macro="input_conditional_genome_file" optional="true"/>
     </inputs>
     <outputs>
         <data name="output" format_source="inputA" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}" />
@@ -88,9 +88,24 @@
                 <param name="operation" value="collapse" />
             </repeat>
             <param name="strand" value="-s" />
-            <param name="genome_choose" value="-g" />
-            <param name="genome_file_opts_selector" value="hist" />
-            <param name="genome" value="mm9.len" ftype="bed" />
+            <conditional name="genome_file_opts">
+                <param name="genome_file_opts_selector" value="hist" />
+                <param name="genome" value="mm9.len" ftype="bed" />
+            </conditional>
+            <output name="output" file="mapBed_result5.bed" ftype="bed" />
+        </test>
+        <test>
+            <param name="inputA" value="mapBed3.bed" ftype="bed" />
+            <param name="inputB" value="mapBed4.bed" ftype="bed" />
+            <repeat name="c_and_o_argument_repeat">
+                <param name="col" value="5" />
+                <param name="operation" value="collapse" />
+            </repeat>
+            <param name="strand" value="-s" />
+            <conditional name="genome_file_opts">
+                <param name="genome_file_opts_selector" value="loc" />
+                <param name="genome" value="mm9"/>
+            </conditional>
             <output name="output" file="mapBed_result5.bed" ftype="bed" />
         </test>
     </tests>