diff get.dists.xml @ 3:56ca2af78a1c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4

--- a/get.dists.xml	Tue Sep 05 16:08:43 2017 -0400
+++ b/get.dists.xml	Wed Feb 14 10:01:30 2018 -0500
@@ -7,23 +7,23 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$accnos" accnos.dat &&
-        ln -s "$input.dist" input.dist.dat &&
+## create symlinks to input datasets
+ln -s '$accnos' accnos.dat &&
+ln -s '$input.dist' input.dist.dat &&
 
-        echo 'get.dists(
-            accnos=accnos.dat,
-            #if $input.source == "phylip":
-                phylip=input.dist.dat
-            #else
-                column=input.dist.dat
-            #end if
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'get.dists(
+    accnos=accnos.dat,
+    #if $input.source == "phylip":
+        phylip=input.dist.dat
+    #else
+        column=input.dist.dat
+    #end if
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <conditional name="input">
@@ -53,8 +53,7 @@
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -65,7 +64,7 @@
 .. _get.dists: https://www.mothur.org/wiki/Get.dists
 
 v.1.20.0: Updated to Mothur 1.33
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>