Mercurial > repos > iuc > mothur_libshuff
diff libshuff.xml @ 2:ffe8649e5434 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 21:59:44 -0400 |
| parents | 590cb2451872 |
| children | eefbe872fd04 |
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--- a/libshuff.xml Tue Sep 05 17:05:02 2017 -0400 +++ b/libshuff.xml Tue Mar 20 21:59:44 2018 -0400 @@ -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"/> @@ -53,6 +53,7 @@ <param name="cutoff" type="float" value="" optional="true" min="0.0" max="1.0" label="cutoff - Cutoff threshold - ignored if left empty"/> </when> </conditional> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -76,6 +77,7 @@ <has_text text="pasture-forest"/> </assert_contents> </output> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test> @@ -98,11 +100,11 @@ <has_text text="pasture-forest"/> </assert_contents> </output> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -113,7 +115,6 @@ .. _libshuff: https://www.mothur.org/wiki/Libshuff -]]> - </help> + ]]></help> <expand macro="citations"/> </tool>