Mercurial > repos > iuc > mothur_get_dists
diff get.dists.xml @ 2:bc5112d1d317 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 21:57:53 -0400 |
| parents | a38b4b058203 |
| children |
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--- a/get.dists.xml Tue Sep 05 16:53:40 2017 -0400 +++ b/get.dists.xml Tue Mar 20 21:57:53 2018 -0400 @@ -7,23 +7,23 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$accnos" accnos.dat && - ln -s "$input.dist" input.dist.dat && +## create symlinks to input datasets +ln -s '$accnos' accnos.dat && +ln -s '$input.dist' input.dist.dat && - echo 'get.dists( - accnos=accnos.dat, - #if $input.source == "phylip": - phylip=input.dist.dat - #else - column=input.dist.dat - #end if - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'get.dists( + accnos=accnos.dat, + #if $input.source == "phylip": + phylip=input.dist.dat + #else + column=input.dist.dat + #end if +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <conditional name="input"> @@ -39,6 +39,7 @@ </when> </conditional> <param name="accnos" type="data" format="mothur.accnos" label="accnos - sort" help="format must be mothur.accnos"/> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -50,11 +51,11 @@ <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/> <param name="accnos" value="amazon.bad.accnos" ftype="mothur.accnos"/> <output name="pick_dist" md5="d853cca7b67723e889a563420f6ccc13" ftype="mothur.square.dist"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -65,7 +66,7 @@ .. _get.dists: https://www.mothur.org/wiki/Get.dists v.1.20.0: Updated to Mothur 1.33 -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>