Mercurial > repos > iuc > mothur_deunique_tree
diff deunique.tree.xml @ 3:6f140b20e011 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:10:19 -0400 |
| parents | 44d01ad18366 |
| children | 283af2e6130c |
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--- a/deunique.tree.xml Fri Sep 08 14:44:27 2017 -0400 +++ b/deunique.tree.xml Tue Mar 20 22:10:19 2018 -0400 @@ -7,23 +7,24 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$tree" tree.dat && - ln -s "$names" names.dat && +## create symlinks to input datasets +ln -s '$tree' tree.dat && +ln -s '$names' names.dat && - echo 'deunique.tree( - tree=tree.dat, - name=names.dat - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'deunique.tree( + tree=tree.dat, + name=names.dat +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="tree" type="data" format="mothur.tre" label="tree - Sequences to filter"/> <param name="names" type="data" format="mothur.names" label="names - Sequences Name reference"/> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -34,11 +35,11 @@ <param name="tree" value="treetest.tre"/> <param name="names" value="treetest.names"/> <output name="out_tree" file="treetest.deunique.tre"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -52,7 +53,6 @@ v1.21.0: Updated to Mothur 1.33 -]]> - </help> + ]]></help> <expand macro="citations"/> </tool>