Mercurial > repos > iuc > mothur_split_abund
diff split.abund.xml @ 3:ef779f6cb288 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:22:51 -0500 |
| parents | 59ab81a8d28d |
| children | 607eee4176b0 |
line wrap: on
line diff
--- a/split.abund.xml Tue Sep 05 16:20:43 2017 -0400 +++ b/split.abund.xml Wed Feb 14 09:22:51 2018 -0500 @@ -7,41 +7,41 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$fasta" fasta.dat && - ln -s "$search.input" search_input.dat && - #if $split.dosplit == "yes": - ln -s "$split.group" split_group.dat && - #end if +## create symlinks to input datasets +ln -s '$fasta' fasta.dat && +ln -s '$search.input' search_input.dat && +#if $split.dosplit == "yes": + ln -s '$split.group' split_group.dat && +#end if - echo 'split.abund( - fasta=fasta.dat, - #if $search.type == "list": - list=search_input.dat, - #if $search.label: - label=${ str($search.label).replace(",","-") }, - #end if - #elif $search.type == "name": - name=search_input.dat, - #else - count=search_input.dat, - #end if - #if $split.dosplit == "yes": - #if $split.group: - group=split_group.dat, - #end if - #if $split.groups: - groups=${ str($split.groups).replace(",","-") }, - #end if - #end if - accnos=$accnos, - cutoff=$cutoff - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'split.abund( + fasta=fasta.dat, + #if $search.type == "list": + list=search_input.dat, + #if $search.label: + label=${ str($search.label).replace(",","-") }, + #end if + #elif $search.type == "name": + name=search_input.dat, + #else + count=search_input.dat, + #end if + #if $split.dosplit == "yes": + #if $split.group: + group=split_group.dat, + #end if + #if $split.groups: + groups=${ str($split.groups).replace(",","-") }, + #end if + #end if + accnos=$accnos, + cutoff=$cutoff +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/> @@ -293,8 +293,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -305,7 +304,7 @@ .. _list: https://www.mothur.org/wiki/List_file .. _name: https://www.mothur.org/wiki/Name_file .. _split.abund: https://www.mothur.org/wiki/Split.abund -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>