Mercurial > repos > iuc > mothur_make_lookup
diff make.lookup.xml @ 3:91652222f7b4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author | iuc |
---|---|
date | Tue, 20 Mar 2018 22:15:22 -0400 |
parents | f338c64b09c1 |
children | d56e5a7a9cef |
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--- a/make.lookup.xml Fri Sep 08 14:55:56 2017 -0400 +++ b/make.lookup.xml Tue Mar 20 22:15:22 2018 -0400 @@ -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"> @@ -53,6 +53,7 @@ <param name="barcode" type="text" value="AACCGTGTC" label="barcode - provide the barcode sequence"/> <param name="key" type="text" value="TCAG" label="key - provide the key sequence"/> <param name="threshold" type="integer" value="10000" min="0" label="threshold - " help=""/> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -69,6 +70,7 @@ <has_line_matching expression="^(-?[(\d\.|nan)]+\t?)+$"/> </assert_contents> </output> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test sanitizers --> @@ -83,11 +85,11 @@ <has_line_matching expression="^(-?[(\d\.|nan)]+\t?)+$"/> </assert_contents> </output> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -97,8 +99,7 @@ .. _make.lookup: https://www.mothur.org/wiki/Make.lookup -]]> - </help> + ]]></help> <citations> <citation type="doi">10.1128/AEM.01541-09</citation> </citations>