diff mapBed.xml @ 34:dde39ba9c031 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95

--- a/mapBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/mapBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,32 +1,34 @@
-<tool id="bedtools_map" name="bedtools MapBed" version="@WRAPPER_VERSION@.2">
+<tool id="bedtools_map" name="bedtools MapBed" version="@TOOL_VERSION@.2">
     <description>apply a function to a column for each overlapping interval</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
+    <command><![CDATA[
 bedtools map
 -a '${inputA}'
 -b '${inputB}'
 $strand
 @C_AND_O_ARGUMENT@
--f $overlap
+@OVERLAP@
+#if str($overlapB):
+    -F $overlapB
+#end if
 $reciprocal
 $split
 $header
 @GENOME_FILE_MAPBED@
 > '${output}'
-]]>
-    </command>
+    ]]></command>
     <inputs>
-        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="File A (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
-        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="File B (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
+        <param name="inputA" argument="-a" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File A (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
+        <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File B (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
         <expand macro="overlap" />
-        <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue=""
+        <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/>
+        <param name="reciprocal" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false"
             label="Require reciprocal overlap"
-            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)" />
+            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" />
         <expand macro="strand2" />
         <expand macro="c_and_o_argument">
             <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" />
@@ -34,7 +36,7 @@
         <expand macro="split" />
         <expand macro="print_header" />
         <conditional name="genome">
-            <param name="genome_choose" argument="-g" type="select" 
+            <param name="genome_choose" argument="-g" type="select"
                 label="Specify a genome file the defines the expected chromosome order in the input files." >
                 <option value="" selected="true">No</option>
                 <option value="-g">Yes</option>
@@ -46,7 +48,7 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format_source="inputA" name="output" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}" />
+        <data name="output" format_source="inputA" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}" />
     </outputs>
     <tests>
         <test>
@@ -101,8 +103,7 @@
             <output name="output" file="mapBed_result5.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedtools map allows one to map overlapping features in a B file onto features in an A file and apply statistics and/or summary operations on those features.
@@ -118,7 +119,6 @@
 The map tool is substantially faster in versions 2.19.0 and later. The plot below demonstrates the increased speed when, for example, counting the number of exome alignments that align to each exon. The bedtools times are compared to the bedops bedmap utility as a point of reference.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>