diff randomBed.xml @ 34:dde39ba9c031 draft

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

--- a/randomBed.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/randomBed.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,30 +1,28 @@
-<tool id="bedtools_randombed" name="bedtools RandomBed" version="@WRAPPER_VERSION@">
+<tool id="bedtools_randombed" name="bedtools RandomBed" version="@TOOL_VERSION@">
     <description>generate random intervals in a genome</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-<![CDATA[
-        bedtools random
-        -g @GENOME_FILE@
-        -l $length
-        -n $intervals
-        #if str($seed.seed_choose) == "True":
-            -seed $seed.seed
-        #end if
-        > "$output"
-]]>
-    </command>
+    <command><![CDATA[
+bedtools random
+-g @GENOME_FILE@
+-l $length
+-n $intervals
+#if str($seed.seed_choose) == "True":
+    -seed $seed.seed
+#end if
+> '$output'
+    ]]></command>
     <inputs>
         <expand macro="input_conditional_genome_file" />
-        <param name="length" type="integer" value="100" label="The length of the intervals to generate" help="(-l)" />
-        <param name="intervals" type="integer" value="1000000" label="The number of intervals to generate" help="(-n)" />
+        <param name="length" argument="-l" type="integer" value="100" label="The length of the intervals to generate" />
+        <param name="intervals" argument="-n" type="integer" value="1000000" label="The number of intervals to generate" />
         <expand macro="seed" />
     </inputs>
     <outputs>
-        <data format="bed" name="output" />
+        <data name="output" format="bed" />
     </outputs>
     <tests>
         <test>
@@ -41,14 +39,12 @@
             </output>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 **What it does**
 
 bedtools random will generate a random set of intervals in BED6 format. One can specify both the number (-n) and the size (-l) of the intervals that should be generated.
 
 @REFERENCES@
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>