Mercurial > repos > iuc > mothur_pca
diff pca.xml @ 3:194d0547e04d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 10:02:00 -0500 |
| parents | 258d04c1c5f8 |
| children | 6fe319c79f31 |
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--- a/pca.xml Tue Sep 05 16:02:57 2017 -0400 +++ b/pca.xml Wed Feb 14 10:02:00 2018 -0500 @@ -7,28 +7,28 @@ <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 'pca( - #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 $groups: - groups=${ str($groups).replace(",","-") }, - #end if - metric=$metric - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'pca( + #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 $groups: + groups=${ str($groups).replace(",","-") }, + #end if + metric=$metric +)' +| 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 Shared or Relabund file"/> @@ -65,8 +65,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -77,7 +76,7 @@ .. _shared: https://www.mothur.org/wiki/Shared_file .. _relabund: https://www.mothur.org/wiki/Get.relabund .. _pca: https://www.mothur.org/wiki/Pca -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>