diff sortBed.xml @ 34:dde39ba9c031 draft

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

--- a/sortBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/sortBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,20 +1,18 @@
-<tool id="bedtools_sortbed" name="bedtools SortBED" version="@WRAPPER_VERSION@">
+<tool id="bedtools_sortbed" name="bedtools SortBED" version="@TOOL_VERSION@">
     <description>order the intervals</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        sortBed
-            -i '$input'
-            $option
-            > '$output'
-]]>
-    </command>
+    <command><![CDATA[
+sortBed
+-i '$input'
+$option
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="Sort the following @STD_BEDTOOLS_INPUT_LABEL@ file"/>
+        <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="Sort the following @STD_BEDTOOLS_INPUT_LABEL@ file" />
         <param name="option" type="select" label="Sort by">
             <!-- sort -k 1,1 -k2,2 -n a.bed -->
             <option value="">chromosome, then by start position (asc)</option>
@@ -27,7 +25,7 @@
         </param>
     </inputs>
     <outputs>
-        <data format_source="input" name="output" metadata_source="input" label="SortBed on ${input.name}"/>
+        <data name="output" format_source="input" metadata_source="input" label="SortBed on ${input.name}"/>
     </outputs>
     <tests>
         <test>
@@ -36,8 +34,7 @@
             <output name="output" file="sortBed_result1.bed" ftype="bed" />
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 Sorts a feature file by chromosome and other criteria.
@@ -50,7 +47,6 @@
 by chromosome then by start position in the following manner: sort -k 1,1 -k2,2 -n a.bed
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>