Mercurial > repos > iuc > mothur_normalize_shared
diff normalize.shared.xml @ 3:6ce70e21be87 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:51:13 -0500 |
| parents | 00df9f248874 |
| children | ad0676e23ef5 |
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--- a/normalize.shared.xml Tue Sep 05 16:28:58 2017 -0400 +++ b/normalize.shared.xml Wed Feb 14 09:51:13 2018 -0500 @@ -7,31 +7,31 @@ <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 'normalize.shared( - #if $otu.is_of_type("mothur.relabund"): - relabund=otu.dat - #elif $otu.is_of_type("mothur.shared"): - shared=otu.dat, - makerelabund=$makerelabund - #end if - #if $label: - ,label=${ str($label).replace(",","-") } - #end if - #if $groups: - ,groups=${ str($groups).replace(",","-") } - #end if - #if $method: - ,method=${ str($method).replace(",","-") } - #end if - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'normalize.shared( + #if $otu.is_of_type("mothur.relabund"): + relabund=otu.dat + #elif $otu.is_of_type("mothur.shared"): + shared=otu.dat, + makerelabund=$makerelabund + #end if + #if $label: + ,label=${ str($label).replace(",","-") } + #end if + #if $groups: + ,groups=${ str($groups).replace(",","-") } + #end if + #if $method: + ,method=${ str($method).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,mothur.relabund" label="shared,relabund - OTU Shared or Relabund file"/> @@ -74,8 +74,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -86,7 +85,7 @@ .. _shared: https://www.mothur.org/wiki/Shared_file .. _relabund: https://www.mothur.org/wiki/Get.relabund .. _normalize.shared: https://www.mothur.org/wiki/Normalize.shared -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>