diff get.group.xml @ 2:0aa74388e4fc draft

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

--- a/get.group.xml	Tue Sep 05 16:56:15 2017 -0400
+++ b/get.group.xml	Tue Mar 20 22:08:52 2018 -0400
@@ -7,26 +7,27 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$otu" otu.dat &&
+## create symlinks to input datasets
+ln -s '$shared' shared.dat &&
 
-        echo 'get.group(
-            shared=otu.dat
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log &&
+echo 'get.group(
+    shared=shared.dat
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log &&
 
-        ## parse relevant output from logfile to file
-        cat mothur.*.logfile
-        | head -n-6
-        | sed '1,29d'
-        > "$bootgroups"
+## parse relevant output from logfile to file
+cat mothur.*.logfile
+| head -n-6
+| sed '1,30d'
+> "$bootgroups"
     ]]></command>
     <inputs>
-        <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
+        <param argument="shared" type="data" format="mothur.shared" label="shared - OTU Shared"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -34,13 +35,13 @@
     </outputs>
     <tests>
         <test>
-            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <param name="shared" value="amazon.an.shared" ftype="mothur.shared"/>
             <output name="bootgroups" md5="93b9f7ead2ee04f056e77b5bb94ea0dd"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -51,7 +52,7 @@
 .. _get.group: https://www.mothur.org/wiki/Get.group
 
 v.1.20.0: Updated to Mothur 1.33
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>