Mercurial > repos > iuc > mothur_indicator
diff indicator.xml @ 4:768bdcfeab90 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:48:25 -0500 |
| parents | 7064503531b8 |
| children | c1250ca75b93 |
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--- a/indicator.xml Fri Sep 08 12:56:04 2017 -0400 +++ b/indicator.xml Wed Feb 14 09:48:25 2018 -0500 @@ -7,40 +7,40 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$otu" otu.dat && - #if $withdesign.tree: - ln -s "$withdesign.tree" withdesign.tree.dat && - #end if - #if $withdesign.havedesign == "yes": - ln -s "$withdesign.design" withdesign.design.dat && - #end if +## create symlinks to input datasets +ln -s '$otu' otu.dat && +#if $withdesign.tree: + ln -s '$withdesign.tree' withdesign.tree.dat && +#end if +#if $withdesign.havedesign == "yes": + ln -s '$withdesign.design' withdesign.design.dat && +#end if - echo 'indicator( - #if $withdesign.tree: - tree=withdesign.tree.dat, - #end if - #if $otu.is_of_type("mothur.relabund"): - relabund=otu.dat, - #elif $otu.is_of_type("mothur.shared"): - shared=otu.dat, - #end if - #if $label: - label=${ str($label).replace(",","-") }, - #end if - #if $withdesign.groups: - groups=${ str($withdesign.groups).replace(",","-") }, - #end if - #if $withdesign.havedesign == "yes": - design=withdesign.design.dat, - #end if - processors='\${GALAXY_SLOTS:-8}' - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'indicator( + #if $withdesign.tree: + tree=withdesign.tree.dat, + #end if + #if $otu.is_of_type("mothur.relabund"): + relabund=otu.dat, + #elif $otu.is_of_type("mothur.shared"): + shared=otu.dat, + #end if + #if $label: + label=${ str($label).replace(",","-") }, + #end if + #if $withdesign.groups: + groups=${ str($withdesign.groups).replace(",","-") }, + #end if + #if $withdesign.havedesign == "yes": + design=withdesign.design.dat, + #end if + processors='\${GALAXY_SLOTS:-8}' +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared/relabund - OTU dataset"/> @@ -137,8 +137,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -151,7 +150,7 @@ .. _indicator: https://www.mothur.org/wiki/Indicator v.1.22.0: Updated to Mothur 1.33 -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>