diff otu.association.xml @ 2:3c42f300324e draft

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

--- a/otu.association.xml	Tue Sep 05 17:18:19 2017 -0400
+++ b/otu.association.xml	Tue Mar 20 22:26:22 2018 -0400
@@ -7,37 +7,37 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$otu" otu.dat &&
-        ln -s "$metadata" metadata.dat &&
+## create symlinks to input datasets
+ln -s '$otu' otu.dat &&
+ln -s '$metadata' metadata.dat &&
 
-        echo 'otu.association(
-            #if $otu.is_of_type("mothur.relabund"):
-                relabund=otu.dat
-            #elif $otu.is_of_type("mothur.shared"):
-                shared=otu.dat
-            #end if
-            #if $label:
-                ,label=${ str($label).replace(",","-") }
-            #end if
-            #if $groups:
-                ,groups=${ str($groups).replace(",","-") }
-            #end if
-            #if $method:
-                ,method=$method
-            #end if
-            #if $metadata:
-                ,metadata=metadata.dat
-            #end if
-            #if $cutoff:
-                ,cutoff=$cutoff
-            #end if
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'otu.association(
+    #if $otu.is_of_type("mothur.relabund"):
+        relabund=otu.dat
+    #elif $otu.is_of_type("mothur.shared"):
+        shared=otu.dat
+    #end if
+    #if $label:
+        ,label=${ str($label).replace(",","-") }
+    #end if
+    #if $groups:
+        ,groups=${ str($groups).replace(",","-") }
+    #end if
+    #if $method:
+        ,method=$method
+    #end if
+    #if $metadata:
+        ,metadata=metadata.dat
+    #end if
+    #if $cutoff:
+        ,cutoff=$cutoff
+    #end if
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/>
@@ -56,6 +56,7 @@
         </param>
         <param name="metadata" type="data" format="tabular" optional="true" label="metadata - find the association between the otus and the metadata."/>
         <param name="cutoff" type="float" value="" min="0" max="1" optional="true" label="cutoff - set a pvalue at which the otu will be reported"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -69,6 +70,7 @@
             <output_collection name="correlations" count="36">
                 <element name="0.41.pearson" md5="ba93b529a7b0e5ca3baa8fe9a41b4107" ftype="mothur.otu.corr"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with relabund file and label and group select -->
@@ -79,11 +81,11 @@
             <output_collection name="correlations" count="5">
                 <element name="0.41.kendall" md5="f01da5dc45d0bae35b692a7306bdc581" ftype="mothur.otu.corr"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -96,7 +98,7 @@
 .. _otu.association: https://www.mothur.org/wiki/Otu.association
 
 v.1.25.0: Updated to mothur 1.33, added cutoff option
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>