diff trim.seqs.xml @ 1:08692ab7170c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9

--- a/trim.seqs.xml	Fri Jun 24 16:53:39 2016 -0400
+++ b/trim.seqs.xml	Thu May 18 18:38:04 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 "$fasta" fasta.dat &&
         ln -s "$names" names.dat &&
@@ -58,6 +61,7 @@
         )'
         | sed 's/ //g'  ## mothur trips over whitespace
         | mothur
+        | tee mothur.out.log
         ## prevent these two files from being gathered into collection
         && mv fasta.trim.fasta fasta.trim
         && mv fasta.scrap.fasta fasta.scrap
@@ -157,11 +161,11 @@
         </test>
         <test><!-- test with count table -->
             <param name="fasta" value="amazon.fasta" ftype="fasta"/>
-            <param name="count" value="amazon.count_table" ftype="mothur.count_table"/>
+            <param name="count" value="amazon1.count_table" ftype="mothur.count_table"/>
             <param name="maxhomop" value="4"/>
             <output name="trim_fasta" md5="14dcaa23735a3f545e7014a69b002859" ftype="fasta"/>
             <output name="scrap_fasta" md5="4f791b7684662f1f962970af46429e24" ftype="fasta"/>
-            <output name="trim_count" md5="2024cbb895f79346606ab196dd130639" ftype="mothur.count_table"/>
+            <output name="trim_count" md5="836b4d72a8cda3741ef435741783b384" ftype="mothur.count_table"/>
             <output name="scrap_count" md5="04ae9f50c1b6f0d8d7e1ac28f845dd4c" ftype="mothur.count_table"/>
             <expand macro="logfile-test"/>
         </test>
@@ -210,11 +214,11 @@
 
 @MOTHUR_OVERVIEW@
 
-**Command Documenation**
+**Command Documentation**
 
 The trim.seqs_ command provides the preprocessing features needed to screen and sort pyrosequences.  The command will enable you to trim off primer sequences and barcodes, use the barcode information to generate a group file and split a fasta file into sub-files, screen sequences based on the qual file that comes from 454 sequencers, cull sequences based on sequence length and the presence of ambiguous bases and get the reverse complement of your sequences. While this analysis is clearly geared towards pyrosequencing collections, it can also be used with traditional Sanger sequences.
 
-.. _trim.seqs: http://www.mothur.org/wiki/Trim.seqs
+.. _trim.seqs: https://www.mothur.org/wiki/Trim.seqs
 
 ]]>
     </help>