Mercurial > repos > iuc > mothur_make_lookup
diff make.lookup.xml @ 4:5aab3adcb3a3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 10:03:24 -0500 |
| parents | ba85750d241d |
| children | d8bc8984cc49 |
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--- a/make.lookup.xml Fri Sep 08 13:25:30 2017 -0400 +++ b/make.lookup.xml Wed Feb 14 10:03:24 2018 -0500 @@ -7,26 +7,26 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - #import re - ## create symlinks to input datasets - ln -s "$reference.template" reference.template.dat && - ln -s "$flow" flow.dat && - ln -s "$error" error.dat && +#import re +## create symlinks to input datasets +ln -s '$reference.template' reference.template.dat && +ln -s '$flow' flow.dat && +ln -s '$error' error.dat && - echo 'make.lookup( - reference=reference.template.dat, - flow=flow.dat, - error=error.dat, - order=$order, - barcode=$re.sub("[^ACTG]","",str($barcode)), - key=$re.sub("[^ACTG]","",str($key)), - threshold=$threshold - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'make.lookup( + reference=reference.template.dat, + flow=flow.dat, + error=error.dat, + order=$order, + barcode=$re.sub("[^ACTG]","",str($barcode)), + key=$re.sub("[^ACTG]","",str($key)), + threshold=$threshold +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <conditional name="reference"> @@ -86,8 +86,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -97,8 +96,7 @@ .. _make.lookup: https://www.mothur.org/wiki/Make.lookup -]]> - </help> + ]]></help> <citations> <citation type="doi">10.1128/AEM.01541-09</citation> </citations>