Mercurial > repos > iuc > mothur_chimera_check

diff chimera.check.xml @ 1:ce8cfbd1c81c 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 04:27:59 -0400
parents 4966028096a3
children 099250d2535e
line wrap: on
line diff
--- a/chimera.check.xml	Fri Jun 24 17:33:26 2016 -0400
+++ b/chimera.check.xml	Fri May 19 04:27:59 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 "$fasta" fasta.dat &&
         ln -s "$alignment.template" alignment.template.dat &&
@@ -26,6 +29,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="fasta" type="data" format="mothur.align" argument="fasta" label="fasta - Candiate Aligned Sequences"/>
@@ -92,13 +96,13 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The chimera.check_ command identifies putative chimeras using the chimeraCheck approach. It looks at distance of left side of query to it's closest match + distance of right side of query to it's closest match - distance of whole query and its closest match over several windows.
 
 Note: following the RDP model this method does not determine whether or not a sequence is chimeric, but allows you to determine that based on the IS values produced.
 
-.. _chimera.check: http://www.mothur.org/wiki/Chimera.check
+.. _chimera.check: https://www.mothur.org/wiki/Chimera.check
 
 ]]>
     </help>