Mercurial > repos > iuc > mothur_cluster_classic
diff cluster.classic.xml @ 1:f8dbdd8fb4bf draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
| author | iuc |
|---|---|
| date | Fri, 19 May 2017 04:25:13 -0400 |
| parents | 1b88f1cd6f5f |
| children | 6af6b54bed72 |
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--- a/cluster.classic.xml Fri Jun 24 17:37:42 2016 -0400 +++ b/cluster.classic.xml Fri May 19 04:25:13 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 "$dist" dist.dat && ln -s "$name" name.dat && @@ -29,9 +32,10 @@ )' | sed 's/ //g' ## mothur trips over whitespace | mothur + | tee mothur.out.log ]]></command> <inputs> - <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix" help="format must be mothur.lower.dist or mothur.square.dist"/> + <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix" help="format must be mothur.lower.dist or mothur.square.dist"/> <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/> <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> <param name="method" type="select" label="method - Select a Clustering Method" help=""> @@ -78,11 +82,11 @@ @MOTHUR_OVERVIEW@ -**Command Documenation** +**Command Documentation** The cluster.classic_ command assign sequences to OTUs (Operational Taxonomy Unit). -.. _cluster.classic: http://www.mothur.org/wiki/Cluster.classic +.. _cluster.classic: https://www.mothur.org/wiki/Cluster.classic ]]> </help>