Mercurial > repos > iuc > mothur_otu_hierarchy
diff otu.hierarchy.xml @ 2:058e6e36f6e5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:20:51 -0400 |
| parents | 7a4200446cbf |
| children | 2e82b56377d8 |
line wrap: on
line diff
--- a/otu.hierarchy.xml Tue Sep 05 17:17:45 2017 -0400 +++ b/otu.hierarchy.xml Tue Mar 20 22:20:51 2018 -0400 @@ -7,19 +7,19 @@ <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 'otu.hierarchy( - list=otu.dat, - label=$label1-$label2, - output=$output - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'otu.hierarchy( + list=otu.dat, + label=$label1-$label2, + output=$output +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="otu" type="data" format="mothur.list" label="list - OTU List"/> @@ -33,6 +33,7 @@ <option value="name" selected="true">OTU sequence names</option> <option value="number">OTU numbers</option> </param> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -44,11 +45,11 @@ <param name="label1" value="0.05"/> <param name="label2" value="0.03"/> <output name="hierarchy" file="amazon.an.0.03.-.0.05.otu.hierarchy" ftype="tabular"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -59,7 +60,6 @@ .. _list: https://www.mothur.org/wiki/List_file .. _otu.hierarchy: https://www.mothur.org/wiki/Otu.hierarchy -]]> - </help> + ]]></help> <expand macro="citations"/> </tool>