Mercurial > repos > iuc > mothur_parse_list
diff parse.list.xml @ 3:fe05fc98c62a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:48:51 -0500 |
| parents | 033b821e30e1 |
| children | 1f3a245edf62 |
line wrap: on
line diff
--- a/parse.list.xml Tue Sep 05 16:38:51 2017 -0400 +++ b/parse.list.xml Wed Feb 14 09:48:51 2018 -0500 @@ -7,26 +7,26 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$otu" otu.dat && - ln -s "$group" group.dat && - ln -s "$count" count.dat && +## create symlinks to input datasets +ln -s '$otu' otu.dat && +ln -s '$group' group.dat && +ln -s '$count' count.dat && - echo 'parse.list( - list=otu.dat, - #if $label: - label=${ str($label).replace(",","-") }, - #end if - #if $count: - count=count.dat, - #end if - group=group.dat - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'parse.list( + list=otu.dat, + #if $label: + label=${ str($label).replace(",","-") }, + #end if + #if $count: + count=count.dat, + #end if + group=group.dat +)' +| 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"/> @@ -59,8 +59,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -73,7 +72,7 @@ .. _parse.list: https://www.mothur.org/wiki/Parse.list v.1.19.0: Updated to mothur 1.33, added count parameter -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>