Mercurial > repos > iuc > mothur_remove_rare
diff remove.rare.xml @ 4:13ef4cafa56d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:22:20 -0500 |
| parents | cc9b225b02e4 |
| children | be26751f7d10 |
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--- a/remove.rare.xml Fri Sep 08 12:58:15 2017 -0400 +++ b/remove.rare.xml Wed Feb 14 09:22:20 2018 -0500 @@ -7,46 +7,46 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$input.otu" input_otu.dat && - #if $input.source == 'list': - ln -s "$input.group" input.group.dat && - ln -s "$input.count" input.count.dat && - #end if +## create symlinks to input datasets +ln -s '$input.otu' input_otu.dat && +#if $input.source == 'list': + ln -s '$input.group' input.group.dat && + ln -s '$input.count' input.count.dat && +#end if - echo 'remove.rare( - #if $input.otu.is_of_type("mothur.rabund"): - rabund=input_otu.dat, - #elif $input.otu.is_of_type("mothur.sabund"): - sabund=input_otu.dat, - #elif $input.otu.is_of_type("mothur.list"): - list=input_otu.dat, - #if $input.group: - group=input.group.dat, - #end if - #if $input.groups: - groups=${ str($input.groups).replace(",","-") }, - #end if - #if $input.count: - count=input.count.dat, - #end if - #elif $input.otu.is_of_type("mothur.shared"): - shared=input_otu.dat, - bygroup=$input.bygroup, - #if $input.groups: - groups=${ str($input.groups).replace(",","-") }, - #end if - #end if - #if $input.label: - label=${ str($input.label).replace(",","-") }, - #end if - nseqs=$nseqs - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'remove.rare( + #if $input.otu.is_of_type("mothur.rabund"): + rabund=input_otu.dat, + #elif $input.otu.is_of_type("mothur.sabund"): + sabund=input_otu.dat, + #elif $input.otu.is_of_type("mothur.list"): + list=input_otu.dat, + #if $input.group: + group=input.group.dat, + #end if + #if $input.groups: + groups=${ str($input.groups).replace(",","-") }, + #end if + #if $input.count: + count=input.count.dat, + #end if + #elif $input.otu.is_of_type("mothur.shared"): + shared=input_otu.dat, + bygroup=$input.bygroup, + #if $input.groups: + groups=${ str($input.groups).replace(",","-") }, + #end if + #end if + #if $input.label: + label=${ str($input.label).replace(",","-") }, + #end if + nseqs=$nseqs +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <conditional name="input"> @@ -144,8 +144,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -159,7 +158,6 @@ .. _shared: https://www.mothur.org/wiki/Shared_file .. _remove.rare: https://www.mothur.org/wiki/Remove.rare -]]> - </help> + ]]></help> <expand macro="citations"/> </tool>