Mercurial > repos > iuc > mothur_libshuff
diff libshuff.xml @ 3:8b4214eada86 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:17:48 -0500 |
| parents | a84c121a3b75 |
| children | af1dd82c53bb |
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--- a/libshuff.xml Tue Sep 05 16:25:51 2017 -0400 +++ b/libshuff.xml Wed Feb 14 09:17:48 2018 -0500 @@ -7,30 +7,30 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$dist" dist.dat && - ln -s "$group" group.dat && +## create symlinks to input datasets +ln -s '$dist' dist.dat && +ln -s '$group' group.dat && - echo 'libshuff( - phylip=dist.dat, - group=group.dat, - #if $groups: - groups=${ str($groups).replace(",","-") }, - #end if - sim=$sim, - #if $form.form2 == "discrete": - step=$form.step, - #if $form.cutoff: - cutoff=$form.cutoff, - #end if - #end if - iters=$iters - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'libshuff( + phylip=dist.dat, + group=group.dat, + #if $groups: + groups=${ str($groups).replace(",","-") }, + #end if + sim=$sim, + #if $form.form2 == "discrete": + step=$form.step, + #if $form.cutoff: + cutoff=$form.cutoff, + #end if + #end if + iters=$iters +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/> @@ -101,8 +101,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -113,7 +112,6 @@ .. _libshuff: https://www.mothur.org/wiki/Libshuff -]]> - </help> + ]]></help> <expand macro="citations"/> </tool>