diff rarefaction.shared.xml @ 1:9bdf0bca01c3 draft

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

--- a/rarefaction.shared.xml	Fri Jun 24 16:45:56 2016 -0400
+++ b/rarefaction.shared.xml	Thu May 18 18:12:18 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 &&
         #if $designc.usedesign == "yes":
@@ -42,6 +45,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
@@ -218,11 +222,11 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
-The rarefaction.shared_ command generates inter-sample rarefaction curves using a re-sampling without replacement approach. The traditional way that ecologists use rarefaction is not to randomize the sampling order within a sample, rather between samples. For instance, if we wanted to know the number of OTUs in the human colon, we might sample from various sites within the colon, and sequence a bunch of 16S rRNA genes. By determining the number of OTUs in each sample and comparing the composition of those samples it is possible to determine how well you have sampled the biodiversity within the individual.  For calc parameter choices see: http://www.mothur.org/wiki/Calculators
+The rarefaction.shared_ command generates inter-sample rarefaction curves using a re-sampling without replacement approach. The traditional way that ecologists use rarefaction is not to randomize the sampling order within a sample, rather between samples. For instance, if we wanted to know the number of OTUs in the human colon, we might sample from various sites within the colon, and sequence a bunch of 16S rRNA genes. By determining the number of OTUs in each sample and comparing the composition of those samples it is possible to determine how well you have sampled the biodiversity within the individual.  For calc parameter choices see: https://www.mothur.org/wiki/Calculators
 
-.. _rarefaction.shared: http://www.mothur.org/wiki/Rarefaction.shared
+.. _rarefaction.shared: https://www.mothur.org/wiki/Rarefaction.shared
 ]]>
     </help>
     <expand macro="citations"/>