Mercurial > repos > iuc > mothur_pca

diff pca.xml @ 1:258d04c1c5f8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 04:55:35 -0400
parents 52a9971dc4fa
children 194d0547e04d
line wrap: on
line diff
--- a/pca.xml	Fri Jun 24 16:44:22 2016 -0400
+++ b/pca.xml	Fri May 19 04:55:35 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 &&
 
@@ -25,6 +28,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/>
@@ -66,13 +70,13 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The pca_ command generate principle components plot data for a shared_ or relabund_ file.
 
-.. _shared: http://www.mothur.org/wiki/Shared_file
-.. _relabund: http://www.mothur.org/wiki/Get.relabund
-.. _pca: http://www.mothur.org/wiki/Pca
+.. _shared: https://www.mothur.org/wiki/Shared_file
+.. _relabund: https://www.mothur.org/wiki/Get.relabund
+.. _pca: https://www.mothur.org/wiki/Pca
 ]]>
     </help>
     <expand macro="citations"/>