diff bed12ToBed6.xml @ 34:dde39ba9c031 draft

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

--- a/bed12ToBed6.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/bed12ToBed6.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,22 +1,20 @@
-<tool id="bedtools_bed12tobed6" name="bedtools BED12 to BED6" version="@WRAPPER_VERSION@">
+<tool id="bedtools_bed12tobed6" name="bedtools BED12 to BED6" version="@TOOL_VERSION@">
     <description>converter</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bed12ToBed6
-        -i '$input'
-        > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+bed12ToBed6
+-i '$input'
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="bed" name="input" type="data" label="Convert the following BED12 file to BED6"/>
+        <param name="input" argument="-i" type="data" format="bed" label="Convert the following BED12 file to BED6"/>
     </inputs>
     <outputs>
-        <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED6)"/>
+        <data name="output" format="bed" metadata_source="input" label="${input.name} (as BED6)"/>
     </outputs>
     <tests>
         <test>
@@ -24,14 +22,12 @@
             <output name="output" file="bed12ToBed6_result1.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bed12ToBed6 is a convenience tool that converts BED features in BED12 (a.k.a. “blocked” BED features such as genes) to discrete BED6 features. For example, in the case of a gene with six exons, bed12ToBed6 would create six separate BED6 features (i.e., one for each exon).
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>