diff spacingBed.xml @ 34:dde39ba9c031 draft

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

--- a/spacingBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/spacingBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,22 +1,20 @@
-<tool id="bedtools_spacingbed" name="bedtools SpacingBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_spacingbed" name="bedtools SpacingBed" version="@TOOL_VERSION@">
     <description>reports the distances between features</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools spacing
-        -i '$input'
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bedtools spacing
+-i '$input'
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="bam,@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@/BAM file"/>
+        <param name="input" argument="-i" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@/BAM file"/>
     </inputs>
     <outputs>
-        <data format_source="input" name="output" metadata_source="input" label="Spaces between intervals of ${input}"/>
+        <data name="output" format_source="input" metadata_source="input" label="Spaces between intervals of ${input}"/>
     </outputs>
     <tests>
         <test>
@@ -24,15 +22,12 @@
             <output name="output" file="spacingBed_result1.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Report the spacing between intervals in a file.
 
-
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>