diff get.rabund.xml @ 2:d441d54fbe09 draft

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

--- a/get.rabund.xml	Tue Sep 05 17:10:39 2017 -0400
+++ b/get.rabund.xml	Tue Mar 20 22:24:06 2018 -0400
@@ -7,37 +7,39 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$count" count.dat &&
-        ln -s "$otu" otu.dat &&
+## create symlinks to input datasets
+ln -s '$count' count.dat &&
+ln -s '$otu' otu.dat &&
 
-        echo 'get.rabund(
-            #if $label:
-                label=${ str($label).replace(",","-") },
-            #end if
-            #if $count:
-                count=count.dat,
-            #end if
-            #if $otu.is_of_type("mothur.list"):
-                list=otu.dat,
-            #elif $otu.is_of_type("mothur.sabund"):
-                sabund=otu.dat,
-            #end if
-            sorted=$sorted
-        )'
-        | sed 's/ //g'  ## mothur trips over whitespace
-        | mothur
-        | tee mothur.out.log
+echo 'get.rabund(
+    #if $label:
+        label=${ str($label).replace(",","-") },
+    #end if
+    #if $count:
+        count=count.dat,
+    #end if
+    #if $otu.is_of_type("mothur.list"):
+        list=otu.dat,
+    #elif $otu.is_of_type("mothur.sabund"):
+        sabund=otu.dat,
+    #end if
+    sorted=$sorted
+)'
+| sed 's/ //g'  ## mothur trips over whitespace
+| mothur
+| tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.list,mothur.sabund" label="list,sabund - List or Sabund"/>
         <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)">
             <expand macro="labeloptions"/>
         </param>
-        <param name="sorted" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sorted - sort by abundance" help="By default the data in the rabund file the same order as the OTUs in input, select to sort by abundance."/>
+        <param name="sorted" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sorted - sort by abundance"
+            help="By default the data in the rabund file the same order as the OTUs in input, select to sort by abundance."/>
         <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"/>
@@ -48,16 +50,17 @@
             <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
             <param name="label" value="0.03,0.05"/>
             <output name="rabund" file="amazon.an.rabund2" ftype="mothur.rabund"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test otu list input -->
             <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
             <output name="rabund" file="amazon.an.rabund" ftype="mothur.rabund"/>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <help><![CDATA[
 
 @MOTHUR_OVERVIEW@
 
@@ -70,7 +73,6 @@
 .. _sabund: https://www.mothur.org/wiki/Sabund_file
 .. _get.rabund: https://www.mothur.org/wiki/Get.rabund
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>