Mercurial > repos > iuc > mothur_split_groups
diff split.groups.xml @ 3:883a95e17395 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 10:10:40 -0500 |
| parents | 87bee516388b |
| children | 7b20827f8e8f |
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--- a/split.groups.xml Tue Sep 05 16:21:21 2017 -0400 +++ b/split.groups.xml Wed Feb 14 10:10:40 2018 -0500 @@ -7,30 +7,30 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$name" name.dat && - ln -s "$count" count.dat && - ln -s "$fasta" fasta.dat && - ln -s "$group" group.dat && +## create symlinks to input datasets +ln -s '$name' name.dat && +ln -s '$count' count.dat && +ln -s '$fasta' fasta.dat && +ln -s '$group' group.dat && - echo 'split.groups( - #if $name: - name=name.dat, - #end if - #if $groups: - groups=${ str($groups).replace(",","-") }, - #end if - #if $count: - count=count.dat, - #end if - fasta=fasta.dat, - group=group.dat - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'split.groups( + #if $name: + name=name.dat, + #end if + #if $groups: + groups=${ str($groups).replace(",","-") }, + #end if + #if $count: + count=count.dat, + #end if + fasta=fasta.dat, + group=group.dat +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="fasta" type="data" format="fasta" label="fasta - Fasta to split by group"/> @@ -61,8 +61,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -73,7 +72,7 @@ .. _group: https://www.mothur.org/wiki/Group_file .. _name: https://www.mothur.org/wiki/Name_file .. _split.groups: https://www.mothur.org/wiki/Split.groups -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>