Mercurial > repos > iuc > mothur_summary_shared
diff summary.shared.xml @ 3:2b8970aa8c5c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:13:21 -0500 |
| parents | 1a4ad79bc1cd |
| children | d98918707cbc |
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--- a/summary.shared.xml Tue Sep 05 16:27:57 2017 -0400 +++ b/summary.shared.xml Wed Feb 14 09:13:21 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 "$otu" otu.dat && +## create symlinks to input datasets +ln -s '$otu' otu.dat && - echo 'summary.shared( - shared=otu.dat, - #if $groups: - label=${ str($label).replace(",","-") }, - #end if - #if $label: - groups=${ str($groups).replace(",","-") }, - #end if - #if $calc: - calc=${ str($calc).replace(",","-") }, - #end if - all=$all, - distance=$distance, - #if $subsample.use == "yes": - #if $subsample.subsample: - subsample=$subsample.subsample, - #else - subsample=T, - #end if - #if $subsample.iters: - iters=$subsample.iters, - #end if - #end if - output=$output, - processors='\${GALAXY_SLOTS:-8}' - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'summary.shared( + shared=otu.dat, + #if $groups: + label=${ str($label).replace(",","-") }, + #end if + #if $label: + groups=${ str($groups).replace(",","-") }, + #end if + #if $calc: + calc=${ str($calc).replace(",","-") }, + #end if + all=$all, + distance=$distance, + #if $subsample.use == "yes": + #if $subsample.subsample: + subsample=$subsample.subsample, + #else + subsample=T, + #end if + #if $subsample.iters: + iters=$subsample.iters, + #end if + #end if + output=$output, + 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" label="shared - OTU Shared"/> @@ -106,7 +106,7 @@ <expand macro="logfile-test"/> </test> <test><!-- test with subsample --> - <param name="otu" value="amazon.an.shared"/> + <param name="otu" value="amazon.mothur.shared"/> <param name="use" value="yes"/> <param name="subsample" value="10"/> <param name="iters" value="42"/> @@ -147,8 +147,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -159,7 +158,7 @@ .. _shared: https://www.mothur.org/wiki/Shared_file .. _group: https://www.mothur.org/wiki/Group_file .. _summary.shared: https://www.mothur.org/wiki/Summary.shared -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>