Mercurial > repos > iuc > mothur_nmds
diff nmds.xml @ 3:ad7485b03fa1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:37:02 -0500 |
| parents | 2af26863e7ca |
| children | 8df78ef3976f |
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--- a/nmds.xml Tue Sep 05 16:25:01 2017 -0400 +++ b/nmds.xml Wed Feb 14 09:37:02 2018 -0500 @@ -7,31 +7,31 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$dist" dist.dat && - ln -s "$axes" axes.dat && +## create symlinks to input datasets +ln -s '$dist' dist.dat && +ln -s '$axes' axes.dat && - echo 'nmds( - phylip=dist.dat - #if $axes: - ,axes=axes.dat - #end if - ,mindim=$mindim - #if $maxdim >= $mindim: - ,maxdim=$maxdim - #end if - ,iters=$iters - ,maxiters=$maxiters +echo 'nmds( + phylip=dist.dat + #if $axes: + ,axes=axes.dat + #end if + ,mindim=$mindim + #if $maxdim >= $mindim: + ,maxdim=$maxdim + #end if + ,iters=$iters + ,maxiters=$maxiters - ## Mothur can't cope with scientific notation - #set epsilon_decimal = "{:.12f}".format(float($epsilon)) - ,epsilon=$epsilon_decimal - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log + ## Mothur can't cope with scientific notation + #set epsilon_decimal = "{:.12f}".format(float($epsilon)) + ,epsilon=$epsilon_decimal +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> @@ -63,8 +63,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -78,7 +77,7 @@ .. _nmds: https://www.mothur.org/wiki/Nmds v1.20.0: Updated to mothur 1.33 -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>