Mercurial > repos > iuc > mothur_indicator
diff indicator.xml @ 1:95175e14cc16 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
| author | iuc |
|---|---|
| date | Thu, 18 May 2017 18:45:13 -0400 |
| parents | 10ae17108e85 |
| children | 7064503531b8 |
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--- a/indicator.xml Fri Jun 24 16:36:02 2016 -0400 +++ b/indicator.xml Thu May 18 18:45:13 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 "$otu" otu.dat && #if $withdesign.tree: @@ -37,6 +40,7 @@ )' | sed 's/ //g' ## mothur trips over whitespace | mothur + | tee mothur.out.log ]]></command> <inputs> <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared/relabund - OTU dataset"/> @@ -138,13 +142,13 @@ @MOTHUR_OVERVIEW@ -**Command Documenation** +**Command Documentation** The indicator_ command reads a shared_ or relabund_ file and a tree file, and outputs a .indicator.summary file and when a tree file is given a .indicator.tre file. The summary file lists the indicator value for each OTU for each node. The new tree contains labels at each internal node. The label is the node number so you can relate the tree to the summary file. -.. _shared: http://www.mothur.org/wiki/Shared_file -.. _relabund: http://www.mothur.org/wiki/Get.relabund -.. _indicator: http://www.mothur.org/wiki/Indicator +.. _shared: https://www.mothur.org/wiki/Shared_file +.. _relabund: https://www.mothur.org/wiki/Get.relabund +.. _indicator: https://www.mothur.org/wiki/Indicator v.1.22.0: Updated to Mothur 1.33 ]]>