Mercurial > repos > iuc > mothur_make_lefse
diff make.lefse.xml @ 3:e9cd4b205ddd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:32:13 -0500 |
| parents | cb917d37d403 |
| children | 4dfe3740f6d6 |
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--- a/make.lefse.xml Tue Sep 05 16:23:57 2017 -0400 +++ b/make.lefse.xml Wed Feb 14 09:32:13 2018 -0500 @@ -7,33 +7,33 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$otu" otu.dat && - ln -s "$design" design.dat && - ln -s "$constaxonomy" constaxonomy.dat && +## create symlinks to input datasets +ln -s '$otu' otu.dat && +ln -s '$design' design.dat && +ln -s '$constaxonomy' constaxonomy.dat && - echo 'make.lefse( - #if $otu.is_of_type("mothur.relabund"): - relabund=otu.dat, - #else - shared=otu.dat, - #end if - #if $design: - design=design.dat, - #end if - #if $constaxonomy: - constaxonomy=constaxonomy.dat, - #end if - #if $label: - label=${ str($label).replace(",","-") }, - #end if - scale=$scale - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'make.lefse( + #if $otu.is_of_type("mothur.relabund"): + relabund=otu.dat, + #else + shared=otu.dat, + #end if + #if $design: + design=design.dat, + #end if + #if $constaxonomy: + constaxonomy=constaxonomy.dat, + #end if + #if $label: + label=${ str($label).replace(",","-") }, + #end if + scale=$scale +)' +| 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 or relabund - provide a shared or relabund file"/> @@ -67,8 +67,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -78,8 +77,7 @@ .. _make.lefse: https://www.mothur.org/wiki/Make.lefse -]]> - </help> + ]]></help> <citations> <citation type="doi">10.1128/AEM.01541-09</citation> </citations>