diff overlapBed.xml @ 34:dde39ba9c031 draft

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

--- a/overlapBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/overlapBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,26 +1,24 @@
-<tool id="bedtools_overlapbed" name="bedtools OverlapBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_overlapbed" name="bedtools OverlapBed" version="@TOOL_VERSION@">
     <description>computes the amount of overlap from two intervals</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools overlap
-        -i '$input'
-        -cols $cols
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools overlap
+-i '$input'
+-cols $cols
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
-        <param name="cols" type="data_column" multiple="True" data_ref="input"
+        <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="cols" type="data_column" data_ref="input" multiple="true"
             label="Specify the columns for the starts and ends of the features for which you’d like to compute the overlap/distance"
             help="The columns must be listed in the following order: start1,end1,start2,end2" />
     </inputs>
     <outputs>
-        <data format_source="input" name="output" metadata_source="input" label="Overlap of ${input.name}"/>
+        <data name="output" format_source="input" metadata_source="input" label="Overlap of ${input.name}"/>
     </outputs>
     <tests>
         <test>
@@ -29,14 +27,12 @@
             <output name="output" file="overlapBed_result1.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 overlap computes the amount of overlap (in the case of positive values) or distance (in the case of negative values) between feature coordinates occurring on the same input line and reports the result at the end of the same line. In this way, it is a useful method for computing custom overlap scores from the output of other BEDTools.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>