diff otu.hierarchy.xml @ 2:058e6e36f6e5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3

--- a/otu.hierarchy.xml	Tue Sep 05 17:17:45 2017 -0400
+++ b/otu.hierarchy.xml	Tue Mar 20 22:20:51 2018 -0400
@@ -7,19 +7,19 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$otu" otu.dat &&
+## create symlinks to input datasets
+ln -s '$otu' otu.dat &&
 
-        echo 'otu.hierarchy(
-            list=otu.dat,
-            label=$label1-$label2,
-            output=$output
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'otu.hierarchy(
+    list=otu.dat,
+    label=$label1-$label2,
+    output=$output
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
@@ -33,6 +33,7 @@
             <option value="name" selected="true">OTU sequence names</option>
             <option value="number">OTU numbers</option>
         </param>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -44,11 +45,11 @@
             <param name="label1" value="0.05"/>
             <param name="label2" value="0.03"/>
             <output name="hierarchy" file="amazon.an.0.03.-.0.05.otu.hierarchy" ftype="tabular"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -59,7 +60,6 @@
 .. _list: https://www.mothur.org/wiki/List_file
 .. _otu.hierarchy: https://www.mothur.org/wiki/Otu.hierarchy
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>