diff rarefaction.single.xml @ 1:3779e72d3525 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9

--- a/rarefaction.single.xml	Fri Jun 24 16:46:10 2016 -0400
+++ b/rarefaction.single.xml	Thu May 18 18:52:12 2017 -0400
@@ -4,8 +4,11 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
+    <expand macro="stdio"/>
     <expand macro="version_command"/>
-    <command detect_errors="aggressive"><![CDATA[
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
         ## create symlinks to input datasets
         ln -s "$otu" otu.dat &&
 
@@ -30,6 +33,12 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
+
+        ## rename output from sobs calculator to be consistent with others
+        #if 'sobs' in str($calc).split(','):
+            && mv otu\.*rarefaction otu.r_sobs
+        #end if
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund,mothur.shared" label="list,rabund,sabund,shared - OTU List"/>
@@ -60,14 +69,14 @@
     <outputs>
         <expand macro="logfile-output"/>
         <collection name="rarefactioncurves" type="list" label="${tool.name} on ${on_string}: rarefaction curves">
-            <discover_datasets pattern=".*?\.groups\.(?P&lt;designation&gt;.*)" format="tabular"/>
+            <discover_datasets pattern=".*?(\.groups)?\.r_(?P&lt;designation&gt;.*)" format="tabular"/>
         </collection>
     </outputs>
     <tests>
         <test><!-- test with default values -->
             <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
             <output_collection name="rarefactioncurves" count="1">
-                <element name="rarefaction" md5="c4c1f1970edf87ea5103e0704130f079" ftype="tabular"/>
+                <element name="sobs" md5="c4c1f1970edf87ea5103e0704130f079" ftype="tabular"/>
             </output_collection>
             <expand macro="logfile-test"/>
         </test>
@@ -76,7 +85,7 @@
             <param name="calc" value="ace,bootstrap,chao,jack,sobs,simpsoneven,shannoneven,heip,smithwilson,coverage,simpson,invsimpson,shannon,npshannon,nseqs"/>
             <param name="label" value="0.03,0.05,0.36,0.55"/>
             <output_collection name="rarefactioncurves" count="15">
-                <element name="r_simpson" md5="8d6b7ad9a68c30c882e93b17d343042a" ftype="tabular"/>
+                <element name="simpson" md5="8d6b7ad9a68c30c882e93b17d343042a" ftype="tabular"/>
             </output_collection>
             <expand macro="logfile-test"/>
         </test>
@@ -86,11 +95,11 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
-The rarefaction.single_ command generates intra-sample rarefaction curves using a re-sampling without replacement approach. Rarefaction curves provide a way of comparing the richness observed in different samples.  For calc parameter choices see: http://www.mothur.org/wiki/Calculators
+The rarefaction.single_ command generates intra-sample rarefaction curves using a re-sampling without replacement approach. Rarefaction curves provide a way of comparing the richness observed in different samples.  For calc parameter choices see: https://www.mothur.org/wiki/Calculators
 
-.. _rarefaction.single: http://www.mothur.org/wiki/Rarefaction.single
+.. _rarefaction.single: https://www.mothur.org/wiki/Rarefaction.single
 ]]>
     </help>
     <expand macro="citations"/>