Mercurial > repos > iuc > mothur_remove_otulabels

diff remove.otulabels.xml @ 1:50874b7ffc15 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:28:32 -0400
parents a88be48a8ddd
children 7bbebc23a901
line wrap: on
line diff
--- a/remove.otulabels.xml	Fri Jun 24 16:47:29 2016 -0400
+++ b/remove.otulabels.xml	Thu May 18 18:28:32 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 "$infile.otu" infile.otu.dat &&
         ln -s "$accnos" accnos.dat &&
@@ -27,12 +30,13 @@
                 shared=infile.otu.dat,
             #end if
             #if $infile.intype == "in_shared" and $infile.label:
-                label=infile.label.dat,
+                label=${ str($infile.label).replace(",","-") },
             #end if
             accnos=accnos.dat
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
     ]]></command>
     <inputs>
         <param name="accnos" type="data" format="mothur.otulabels" label="accnos - otulabels" help="Required"/>
@@ -62,7 +66,7 @@
             <param name="intype" value="in_shared"/>
             <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
             <param name="label" value="0.22"/>
-            <ouptut name="pick_out" md5="8ab2a6afd9a2547e3c4ffe2e83375c33" ftype="mothur.list"/>
+            <output name="pick_out" md5="8ab2a6afd9a2547e3c4ffe2e83375c33" ftype="mothur.list"/>
             <expand macro="logfile-test"/>
         </test>
         <test><!-- test with constaxonomy/otucorr/corraxes file -->
@@ -78,14 +82,14 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The remove.otulabels_ command removes otu labels from the output from classify.otu_, corr.axes_ and otu.association_. This can be useful especially with subsampled datasets or when groups have been selected.
 
-.. _classify.otu: http://www.mothur.org/wiki/Classify.otu
-.. _corr.axes: http://www.mothur.org/wiki/Corr.axes
-.. _otu.association: http://www.mothur.org/wiki/Otu.association
-.. _remove.otulabels: http://www.mothur.org/wiki/Remove.otulabels
+.. _classify.otu: https://www.mothur.org/wiki/Classify.otu
+.. _corr.axes: https://www.mothur.org/wiki/Corr.axes
+.. _otu.association: https://www.mothur.org/wiki/Otu.association
+.. _remove.otulabels: https://www.mothur.org/wiki/Remove.otulabels
 ]]>
     </help>
     <expand macro="citations"/>