Mercurial > repos > iuc > mothur_classify_tree
diff classify.tree.xml @ 1:c51b7f1f7972 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
| author | iuc |
|---|---|
| date | Fri, 19 May 2017 04:26:00 -0400 |
| parents | 2acbb5457141 |
| children | 61b024f58c48 |
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--- a/classify.tree.xml Fri Jun 24 17:37:15 2016 -0400 +++ b/classify.tree.xml Fri May 19 04:26:00 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 "$tree" tree.dat && ln -s "$name" name.dat && @@ -24,6 +27,7 @@ )' | sed 's/ //g' ## mothur trips over whitespace | mothur + | tee mothur.out.log ]]></command> <inputs> <param name="taxonomy" type="data" format="mothur.ref.taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/> @@ -52,7 +56,7 @@ @MOTHUR_OVERVIEW@ -**Command Documenation** +**Command Documentation** The classify.tree_ command is used to get a consensus taxonomy for each node on a tree. Input is a taxonomy_ and a tree_ with optional name_ or group_ reference. @@ -65,11 +69,11 @@ ... -.. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline +.. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline .. _tree: http://evolution.genetics.washington.edu/phylip/newicktree.html -.. _name: http://www.mothur.org/wiki/Name_file -.. _group: http://www.mothur.org/wiki/Group_file -.. _classify.tree: http://www.mothur.org/wiki/Classify.tree +.. _name: https://www.mothur.org/wiki/Name_file +.. _group: https://www.mothur.org/wiki/Group_file +.. _classify.tree: https://www.mothur.org/wiki/Classify.tree v.1.25.0: Trivial upgrade to Mothur 1.33 ]]>