diff expandBed.xml @ 34:dde39ba9c031 draft

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

--- a/expandBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/expandBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,24 +1,22 @@
-<tool id="bedtools_expandbed" name="bedtools ExpandBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_expandbed" name="bedtools ExpandBed" version="@TOOL_VERSION@">
     <description>replicate lines based on lists of values in columns</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools expand
-        -c "${cols}"
-        -i "${input}"
-        > "${output}"
-]]>
-    </command>
+    <command><![CDATA[
+bedtools expand
+-c '${cols}'
+-i '${input}'
+> '${output}'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
         <expand macro="choose_columns" />
     </inputs>
     <outputs>
-        <data name="output" metadata_source="input" format_source="input" />
+        <data name="output" format_source="input" metadata_source="input" />
     </outputs>
     <tests>
         <test>
@@ -32,14 +30,12 @@
             <output name="output" file="expandBed_result2.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Replicate lines in a file based on columns of comma-separated values.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>