Mercurial > repos > iuc > mothur_cooccurrence
diff cooccurrence.xml @ 3:1bebb226e793 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:16:00 -0500 |
| parents | 72f9b9aca28d |
| children | 7947bd3c6e8a |
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--- a/cooccurrence.xml Tue Sep 05 16:38:28 2017 -0400 +++ b/cooccurrence.xml Wed Feb 14 09:16:00 2018 -0500 @@ -7,26 +7,26 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$otu" otu.dat && +## create symlinks to input datasets +ln -s '$otu' otu.dat && - echo 'cooccurrence( - shared=otu.dat, - metric=$metric, - matrixmodel=$matrixmodel, - iters=$iters - #if $label: - ,label=${ str($label).replace(",","-") } - #end if - #if $groups: - ,groups=${ str($groups).replace(",","-") } - #end if - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'cooccurrence( + shared=otu.dat, + metric=$metric, + matrixmodel=$matrixmodel, + iters=$iters + #if $label: + ,label=${ str($label).replace(",","-") } + #end if + #if $groups: + ,groups=${ str($groups).replace(",","-") } + #end if +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared file"/> @@ -90,8 +90,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -162,7 +161,7 @@ .. _cooccurrence: https://www.mothur.org/wiki/Cooccurrence v1.26.0: Updated to Mothur 1.33 -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>