changeset 31:e19bebe96cd2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 39701b6cbb7a45ec45f1545648b73a6b8ed3e184

--- a/mapBed.xml	Fri Aug 17 05:42:39 2018 -0400
+++ b/mapBed.xml	Tue Nov 20 10:34:42 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="bedtools_map" name="MapBed" version="@WRAPPER_VERSION@.0">
+<tool id="bedtools_map" name="MapBed" version="@WRAPPER_VERSION@.1">
     <description>apply a function to a column for each overlapping interval</description>
     <macros>
         <import>macros.xml</import>
@@ -7,17 +7,17 @@
     <expand macro="stdio" />
     <command>
 <![CDATA[
-        bedtools map
-        -a '${inputA}'
-        -b '${inputB}'
-        $strand
-        @C_AND_O_ARGUMENT@
-        -f $overlap
-        $reciprocal
-        $split
-        $header
-        @GENOME_FILE_MAPBED@
-        > "${output}"
+bedtools map
+-a '${inputA}'
+-b '${inputB}'
+$strand
+@C_AND_O_ARGUMENT@
+-f $overlap
+$reciprocal
+$split
+$header
+@GENOME_FILE_MAPBED@
+> '${output}'
 ]]>
     </command>
     <inputs>
@@ -29,7 +29,7 @@
             help="If set, the overlap between the BAM alignment and the BED interval must affect the above fraction of both the alignment and the BED interval. (-r)" />
         <expand macro="strand2" />
         <expand macro="c_and_o_argument">
-            <param name="col" type="data_column" data_ref="inputA" label="Specify the column(s) that should be summarized" help="(-c)" />
+            <param name="col" argument="-c" type="data_column" data_ref="inputB" label="Specify the column(s) from the B file to map onto intervals in A" help="Multiple columns can be specified in a comma-delimited list" />
         </expand>
         <expand macro="split" />
         <expand macro="print_header" />