diff pcoa.xml @ 2:3c560e5c3dd2 draft

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

--- a/pcoa.xml	Tue Sep 05 17:04:23 2017 -0400
+++ b/pcoa.xml	Tue Mar 20 22:18:05 2018 -0400
@@ -7,22 +7,23 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$phylip" phylip.dat &&
+## create symlinks to input datasets
+ln -s '$phylip' phylip.dat &&
 
-        echo 'pcoa(
-            phylip=phylip.dat,
-            metric=$metric
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'pcoa(
+    phylip=phylip.dat,
+    metric=$metric
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Phylip Distance Matrix"/>
         <param name="metric" type="boolean" truevalue="true" falsevalue="false" checked="true" label="metric - Calculate pearson correlation coefficient"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -34,11 +35,11 @@
             <param name="phylip" value="amazon.dist"/>
             <output name="pcoa" file="amazon.pcoa.axes"/>
             <output name="loadings" file="amazon.pcoa.loadings"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -48,7 +49,7 @@
 
 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
 .. _pcoa: https://www.mothur.org/wiki/Pcoa
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>