diff phylotype.xml @ 2:f750e0c2c7f9 draft

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

--- a/phylotype.xml	Tue Sep 05 17:12:52 2017 -0400
+++ b/phylotype.xml	Tue Mar 20 22:17:49 2018 -0400
@@ -7,27 +7,27 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$taxonomy" taxonomy.dat &&
-        ln -s "$name" name.dat &&
+## create symlinks to input datasets
+ln -s '$taxonomy' taxonomy.dat &&
+ln -s '$name' name.dat &&
 
-        echo 'phylotype(
-            taxonomy=taxonomy.dat
-            #if $cutoff:
-                ,cutoff=$cutoff
-            #end if
-            #if $name:
-                ,name=name.dat
-            #end if
-            #if $label:
-                ,label=${ str($label).replace(",","-") }
-            #end if
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'phylotype(
+    taxonomy=taxonomy.dat
+    #if $cutoff:
+        ,cutoff=$cutoff
+    #end if
+    #if $name:
+        ,name=name.dat
+    #end if
+    #if $label:
+        ,label=${ str($label).replace(",","-") }
+    #end if
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy"/>
@@ -46,6 +46,7 @@
             <option value="10">10</option>
         </param>
         <param name="cutoff" type="integer" value="" min="0" max="50" optional="true" label="cutoff - Truncate the taxonomy at depth (Ignored if &lt; 0)"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -59,6 +60,7 @@
             <output name="rabund" md5="689fb6fd2fb4cd0740fc8b62d7e05556" ftype="mothur.rabund"/>
             <output name="sabund" md5="62547e84f1d051a16937715433f3d78a" ftype="mothur.sabund"/>
             <output name="otulist" md5="c808112d524863bbc973dd721ba18a06" ftype="mothur.list"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test>
@@ -68,11 +70,11 @@
             <output name="rabund" md5="3d2e3821bef6ecd7eaf0ea62e8692154" ftype="mothur.rabund"/>
             <output name="sabund" md5="582825c475bffbf7e450156ff26c844a" ftype="mothur.sabund"/>
             <output name="otulist" md5="424a2c62df2e37b32542731b9631f8ed" ftype="mothur.list"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -85,7 +87,6 @@
 .. _sabund: https://www.mothur.org/wiki/Sabund_file
 .. _phylotype: https://www.mothur.org/wiki/Phylotype
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>