Mercurial > repos > iuc > mothur_degap_seqs

diff degap.seqs.xml @ 1:7e334883931c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author: iuc
date: Thu, 18 May 2017 18:11:48 -0400
parents: ae5e88c4d82b
children: de6d0eaca0ed
--- a/degap.seqs.xml	Fri Jun 24 16:29:07 2016 -0400
+++ b/degap.seqs.xml	Thu May 18 18:11:48 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 "$fasta" fasta.dat &&
 
@@ -14,6 +17,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="fasta" label="fasta - Dataset"/>
@@ -34,11 +38,11 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The degap.seqs_ command reads a fasta file and outputs a fasta containing the sequences after all gap characters are removed.
 
-.. _degap.seqs: http://www.mothur.org/wiki/Degap.seqs
+.. _degap.seqs: https://www.mothur.org/wiki/Degap.seqs
 
 v1.21.0: Updated to Mothur 1.33