Mercurial > repos > iuc > mothur_classify_seqs
diff classify.seqs.xml @ 1:7c45c65f957b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
| author | iuc |
|---|---|
| date | Thu, 18 May 2017 18:10:02 -0400 |
| parents | 0b58880da760 |
| children | af9313bec520 |
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--- a/classify.seqs.xml Fri Jun 24 17:36:48 2016 -0400 +++ b/classify.seqs.xml Thu May 18 18:10:02 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@ + ## enable mothur to find blast loc=`which mothur` && ln -s "\${loc%/mothur}"/* . && @@ -14,6 +17,7 @@ ln -s "$alignment.template" alignment.template.dat && ln -s "$tax.taxonomy" tax.taxonomy.dat && ln -s "$count" count.dat && + ln -s "$name" name.dat && echo 'classify.seqs( fasta=fasta.dat, @@ -40,11 +44,15 @@ #if $count: count=count.dat, #end if + #if $name: + name=name.dat, + #end if relabund=$relabund, processors='\${GALAXY_SLOTS:-8}' )' | sed 's/ //g' ## mothur trips over whitespace | ./mothur + | tee mothur.out.log ]]></command> <inputs> <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/> @@ -112,6 +120,7 @@ </when> </conditional> <param name="count" type="data" format="mothur.count_table" label="count file" optional="true"/> + <param name="name" type="data" format="mothur.names" label="names file" optional="true"/> <param name="relabund" type="boolean" falsevalue="false" truevalue="true" checked="false" label="relabund - allows you to indicate that you want the summary files to be relative abundances rather than raw abundances. default=f"/> </inputs> <outputs> @@ -166,11 +175,11 @@ @MOTHUR_OVERVIEW@ -**Command Documenation** +**Command Documentation** The classify.seqs_ command assigns sequences to chosen taxonomy outline. -.. _classify.seqs: http://www.mothur.org/wiki/Classify.seqs +.. _classify.seqs: https://www.mothur.org/wiki/Classify.seqs v1.22.0: Updated for Mothur 1.33. Added count parameter (1.28), added relabund parameter (1.33), bayesian term changed to wang.