diff mergeBed.xml @ 34:dde39ba9c031 draft

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

--- a/mergeBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/mergeBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,39 +1,37 @@
-<tool id="bedtools_mergebed" name="bedtools MergeBED" version="@WRAPPER_VERSION@">
+<tool id="bedtools_mergebed" name="bedtools MergeBED" version="@TOOL_VERSION@">
     <description>combine overlapping/nearby intervals into a single interval</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        mergeBed
-            -i "${input}"
-            $strand
-            -d $distance
-            $header
-            @C_AND_O_ARGUMENT@
-            > "${output}"
-]]>
-    </command>
+    <command><![CDATA[
+mergeBed
+-i '${input}'
+$strand
+-d $distance
+$header
+@C_AND_O_ARGUMENT@
+> '${output}'
+    ]]></command>
     <inputs>
-        <param  name="input" format="bam,@STD_BEDTOOLS_INPUTS@" type="data" label="Sort the following BAM/@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param  name="input" argument="-i" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="Sort the following BAM/@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <param name="strand" type="select" label="Calculation based on strandedness?">
-            <option value="" selected="True">Overlaps on either strand</option>
-            <option value="-s">Force strandedness. That is, only merge features that are the same strand.</option>
-            <option value="-S +">Force merge for forward strand only.</option>
-            <option value="-S -">Force merge for reverse strand only.</option>
+            <option value="" selected="true">Overlaps on either strand</option>
+            <option value="-s">Force strandedness. That is, only merge features that are the same strand (-s)</option>
+            <option value="-S +">Force merge for forward strand only (-S +)</option>
+            <option value="-S -">Force merge for reverse strand only (-S -)</option>
         </param>
-        <param name="distance" type="integer" value="0"
+        <param name="distance" argument="-d" type="integer" value="0"
             label="Maximum distance between features allowed for features to be merged"
-            help="That is, overlapping and/or book-ended features are merged. (-d)"/>
+            help="That is, overlapping and/or book-ended features are merged"/>
         <expand macro="print_header" />
         <expand macro="c_and_o_argument">
-            <param name="col" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" help="(-c)" />
+            <param name="col" argument="-c" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" />
         </expand>
     </inputs>
     <outputs>
-        <data format="bed" name="output" metadata_source="input" label="Merged ${input.name}"/>
+        <data name="output" format="bed" metadata_source="input" label="Merged ${input.name}"/>
     </outputs>
     <tests>
         <test>
@@ -65,8 +63,7 @@
             <output name="output" file="mergedBed_result5.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedtools merge combines overlapping or "book-ended" features in an interval file into a single feature which spans all of the combined features.
@@ -143,7 +140,6 @@
 
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>