Mercurial > repos > iuc > mothur_pcoa
diff pcoa.xml @ 2:3c560e5c3dd2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:18:05 -0400 |
| parents | 57b46e1032ad |
| children | c9fc98593dec |
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--- a/pcoa.xml Tue Sep 05 17:04:23 2017 -0400 +++ b/pcoa.xml Tue Mar 20 22:18:05 2018 -0400 @@ -7,22 +7,23 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$phylip" phylip.dat && +## create symlinks to input datasets +ln -s '$phylip' phylip.dat && - echo 'pcoa( - phylip=phylip.dat, - metric=$metric - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'pcoa( + phylip=phylip.dat, + metric=$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"/> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -34,11 +35,11 @@ <param name="phylip" value="amazon.dist"/> <output name="pcoa" file="amazon.pcoa.axes"/> <output name="loadings" file="amazon.pcoa.loadings"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -48,7 +49,7 @@ .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix .. _pcoa: https://www.mothur.org/wiki/Pcoa -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>