diff chop.seqs.xml @ 1:b0f422397f42 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d

--- a/chop.seqs.xml	Fri Jun 24 17:35:55 2016 -0400
+++ b/chop.seqs.xml	Fri May 19 04:22:24 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 "$fasta" fasta.dat &&
         ln -s "$name" name.dat &&
@@ -31,6 +34,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to be chopped"/>
@@ -62,11 +66,11 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The chop.seqs_ command reads a fasta file of sequences and outputs a .chop.fasta file containing the trimmed sequences. It works on both aligned and unaligned sequences.
 
-.. _chop.seqs: http://www.mothur.org/wiki/Chop.seqs
+.. _chop.seqs: https://www.mothur.org/wiki/Chop.seqs
 
 v1.20.0: Updated to 1.33. Added name, group and count options for mothur version 1.31.0
 ]]>