diff parse.list.xml @ 2:65ce515b9645 draft

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

--- a/parse.list.xml	Tue Sep 05 17:12:39 2017 -0400
+++ b/parse.list.xml	Tue Mar 20 22:25:29 2018 -0400
@@ -7,26 +7,26 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$otu" otu.dat &&
-        ln -s "$group" group.dat &&
-        ln -s "$count" count.dat &&
+## create symlinks to input datasets
+ln -s '$otu' otu.dat &&
+ln -s '$group' group.dat &&
+ln -s '$count' count.dat &&
 
-        echo 'parse.list(
-            list=otu.dat,
-            #if $label:
-                label=${ str($label).replace(",","-") },
-            #end if
-            #if $count:
-                count=count.dat,
-            #end if
-            group=group.dat
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'parse.list(
+    list=otu.dat,
+    #if $label:
+        label=${ str($label).replace(",","-") },
+    #end if
+    #if $count:
+        count=count.dat,
+    #end if
+    group=group.dat
+)'
+| 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"/>
@@ -35,6 +35,7 @@
             <expand macro="labeloptions"/>
         </param>
         <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
+        <expand macro="param-savelog"/>
     </inputs>
     <outputs>
         <expand macro="logfile-output"/>
@@ -49,6 +50,7 @@
             <output_collection name="listfiles" count="72">
                 <element name="pasture.0.21" md5="5c803fd0f0e1de69c51048e02bc02e65" ftype="mothur.list"/>
             </output_collection>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test>
@@ -56,11 +58,11 @@
             <param name="group" value="amazon.groups" ftype="mothur.groups"/>
             <param name="label" value="0.03,0.05"/>
             <output_collection name="listfiles" count="4"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -73,7 +75,7 @@
 .. _parse.list: https://www.mothur.org/wiki/Parse.list
 
 v.1.19.0: Updated to mothur 1.33, added count parameter
-]]>
-    </help>
+
+    ]]></help>
     <expand macro="citations"/>
 </tool>