Mercurial > repos > iuc > mothur_tree_shared
diff tree.shared.xml @ 3:8d6cd6767107 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:37:37 -0500 |
| parents | a16c10c1c418 |
| children | 466897b7c726 |
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--- a/tree.shared.xml Tue Sep 05 16:09:08 2017 -0400 +++ b/tree.shared.xml Wed Feb 14 09:37:37 2018 -0500 @@ -7,52 +7,52 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$input.dist" input_dist.dat && - #if not $input.source == "shared": - ln -s "$input.name" input_name.dat && - #end if +## create symlinks to input datasets +ln -s '$input.dist' input_dist.dat && +#if not $input.source == "shared": + ln -s '$input.name' input_name.dat && +#end if - echo 'tree.shared( - #if $input.source == "shared": - shared=input_dist.dat, - #if $input.groups: - groups=${ str($input.groups).replace(",","-") }, - #end if - #if $input.label: - label=${ str($input.label).replace(",","-") }, - #end if - #if $input.subsampling.use == "yes": - #if $input.subsampling.subsample: - subsample=$input.subsampling.subsample, - #else - subsample=T, - #end if - #if $input.subsampling.iters: - iters="$input.subsampling.iters, - #end if - #end if - #elif $input.source == "column": - column=input_dist.dat, - name=input_name.dat, - #elif $input.source == "phylip": - phylip=input_dist.dat, - #if $input.name: - name=input_name.dat, - #end if +echo 'tree.shared( + #if $input.source == "shared": + shared=input_dist.dat, + #if $input.groups: + groups=${ str($input.groups).replace(",","-") }, + #end if + #if $input.label: + label=${ str($input.label).replace(",","-") }, + #end if + #if $input.subsampling.use == "yes": + #if $input.subsampling.subsample: + subsample=$input.subsampling.subsample, #else - count=input_name.dat, + subsample=T, #end if - #if $calc: - calc=${ str($calc).replace(",","-") }, + #if $input.subsampling.iters: + iters="$input.subsampling.iters, #end if - processors='\${GALAXY_SLOTS:-8}' - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log + #end if + #elif $input.source == "column": + column=input_dist.dat, + name=input_name.dat, + #elif $input.source == "phylip": + phylip=input_dist.dat, + #if $input.name: + name=input_name.dat, + #end if + #else + count=input_name.dat, + #end if + #if $calc: + calc=${ str($calc).replace(",","-") }, + #end if + processors='\${GALAXY_SLOTS:-8}' +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <conditional name="input"> @@ -152,8 +152,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -163,7 +162,6 @@ .. _tree.shared: https://www.mothur.org/wiki/Tree.shared -]]> - </help> + ]]></help> <expand macro="citations"/> </tool>