Mercurial > repos > iuc > mothur_pcoa
diff pcoa.xml @ 0:57b46e1032ad draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
| author | iuc |
|---|---|
| date | Fri, 19 May 2017 05:01:28 -0400 |
| parents | |
| children | 3c560e5c3dd2 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pcoa.xml Fri May 19 05:01:28 2017 -0400 @@ -0,0 +1,54 @@ +<tool profile="16.07" id="mothur_pcoa" name="Pcoa" version="@WRAPPER_VERSION@.0"> + <description>Principal Coordinate Analysis for a distance matrix</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <expand macro="version_command"/> + <command><![CDATA[ + @SHELL_OPTIONS@ + + ## create symlinks to input datasets + ln -s "$phylip" phylip.dat && + + echo 'pcoa( + phylip=phylip.dat, + metric=$metric + )' + | sed 's/ //g' ## mothur trips over whitespace + | mothur + | tee mothur.out.log + ]]></command> + <inputs> + <param name="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Phylip Distance Matrix"/> + <param name="metric" type="boolean" truevalue="true" falsevalue="false" checked="true" label="metric - Calculate pearson correlation coefficient"/> + </inputs> + <outputs> + <expand macro="logfile-output"/> + <data name="pcoa" format="mothur.axes" from_work_dir="phylip*.pcoa.axes" label="${tool.name} on ${on_string}: pcoa.axes"/> + <data name="loadings" format="tabular" from_work_dir="phylip*.pcoa.loadings" label="${tool.name} on ${on_string}: loadings"/> + </outputs> + <tests> + <test> + <param name="phylip" value="amazon.dist"/> + <output name="pcoa" file="amazon.pcoa.axes"/> + <output name="loadings" file="amazon.pcoa.loadings"/> + <expand macro="logfile-test"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +**Command Documentation** + +The pcoa_ command performs principal coordinate analysis on a phylip-formatted_distance_matrix_. + +.. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix +.. _pcoa: https://www.mothur.org/wiki/Pcoa +]]> + </help> + <expand macro="citations"/> +</tool>