Mercurial > repos > iuc > mothur_cluster
diff cluster.xml @ 1:c212b5d35bfe draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
| author | iuc |
|---|---|
| date | Fri, 19 May 2017 05:08:26 -0400 |
| parents | 5d1b3989db21 |
| children | d7782c32375c |
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--- a/cluster.xml Fri Jun 24 16:26:41 2016 -0400 +++ b/cluster.xml Fri May 19 05:08:26 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 "$matrix.dist" matrix.dist.dat && ln -s "$matrix.name" matrix.name.dat && @@ -33,6 +36,7 @@ )' | sed 's/ //g' ## mothur trips over whitespace | mothur + | tee mothur.out.log ]]></command> <inputs> <conditional name="matrix"> @@ -42,10 +46,10 @@ </param> <when value="column"> <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/> - <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/> + <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> </when> <when value="phylip"> - <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> + <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> </when> </conditional> @@ -98,17 +102,17 @@ @MOTHUR_OVERVIEW@ -**Command Documenation** +**Command Documentation** The cluster_ command assign sequences to OTUs (Operational Taxonomy Unit). The assignment is based on a phylip-formatted_distance_matrix_ or a column-formatted_distance_matrix_ and name_ file. It generates a list_, a sabund_ (Species Abundance), and a rabund_ (Relative Abundance) file. -.. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix -.. _column-formatted_distance_matrix: http://www.mothur.org/wiki/Column-formatted_distance_matrix -.. _name: http://www.mothur.org/wiki/Name_file -.. _list: http://www.mothur.org/wiki/List_file -.. _rabund: http://www.mothur.org/wiki/Rabund_file -.. _sabund: http://www.mothur.org/wiki/Sabund_file -.. _cluster: http://www.mothur.org/wiki/Cluster +.. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix +.. _column-formatted_distance_matrix: https://www.mothur.org/wiki/Column-formatted_distance_matrix +.. _name: https://www.mothur.org/wiki/Name_file +.. _list: https://www.mothur.org/wiki/List_file +.. _rabund: https://www.mothur.org/wiki/Rabund_file +.. _sabund: https://www.mothur.org/wiki/Sabund_file +.. _cluster: https://www.mothur.org/wiki/Cluster ]]> </help>