Mercurial > repos > iuc > mothur_remove_lineage
diff remove.lineage.xml @ 3:702f118f52f9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:25:48 -0500 |
| parents | b4939bc52ca7 |
| children | 3a7f96ed57ff |
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--- a/remove.lineage.xml Tue Sep 05 16:41:21 2017 -0400 +++ b/remove.lineage.xml Wed Feb 14 09:25:48 2018 -0500 @@ -7,63 +7,63 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - #import re - ## create symlinks to input datasets - ln -s "$file.taxonomy" file.taxonomy.dat && - #if $file.filetype == "useconstaxonomy": - ln -s "$file.shared" file.shared.dat && - ln -s "$file.list" file.list.dat && - #end if - ln -s "$fasta_in" fasta_in.dat && - ln -s "$group_in" group_in.dat && - ln -s "$alignreport_in" alignreport_in.dat && - ln -s "$list_in" list_in.dat && - ln -s "$name_in" name_in.dat && - ln -s "$count" count.dat && +#import re +## create symlinks to input datasets +ln -s '$file.taxonomy' file.taxonomy.dat && +#if $file.filetype == "useconstaxonomy": + ln -s '$file.shared' file.shared.dat && + ln -s '$file.list' file.list.dat && +#end if +ln -s '$fasta_in' fasta_in.dat && +ln -s '$group_in' group_in.dat && +ln -s '$alignreport_in' alignreport_in.dat && +ln -s '$list_in' list_in.dat && +ln -s '$name_in' name_in.dat && +ln -s '$count' count.dat && - echo 'remove.lineage( - #if $file.filetype == "usetaxonomy": - taxonomy=file.taxonomy.dat - #else - constaxonomy=file.taxonomy.dat - #if $file.shared: - ,shared=file.shared.dat - #end if - #if $file.list: - ,list=file.list.dat - #end if - #end if - #if $file.taxons: - #set taxonstring=str($file.taxons).replace(",","-") - ,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxonstring ))'"' - #elif $taxon: - ,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxon.value )).replace(",","-")'"' - #end if - #if $fasta_in: - ,fasta=fasta_in.dat - #end if - #if $group_in: - ,group=group_in.dat - #end if - #if $alignreport_in: - ,alignreport=alignreport_in.dat - #end if - #if $list_in: - ,list=list_in.dat - #end if - #if $name_in: - ,name=name_in.dat - ,dups=$dups - #end if - #if $count: - ,count=count.dat - #end if - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'remove.lineage( + #if $file.filetype == "usetaxonomy": + taxonomy=file.taxonomy.dat + #else + constaxonomy=file.taxonomy.dat + #if $file.shared: + ,shared=file.shared.dat + #end if + #if $file.list: + ,list=file.list.dat + #end if + #end if + #if $file.taxons: + #set taxonstring=str($file.taxons).replace(",","-") + ,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxonstring ))'"' + #elif $taxon: + ,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxon.value )).replace(",","-")'"' + #end if + #if $fasta_in: + ,fasta=fasta_in.dat + #end if + #if $group_in: + ,group=group_in.dat + #end if + #if $alignreport_in: + ,alignreport=alignreport_in.dat + #end if + #if $list_in: + ,list=list_in.dat + #end if + #if $name_in: + ,name=name_in.dat + ,dups=$dups + #end if + #if $count: + ,count=count.dat + #end if +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <conditional name="file"> @@ -190,8 +190,7 @@ <output name="taxonomy_out" md5="017f53dd82f3e1afcf48778034b51685"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -206,7 +205,6 @@ .. _align.report: https://www.mothur.org/wiki/Align.seqs .. _remove.lineage: https://www.mothur.org/wiki/Remove.lineage -]]> - </help> + ]]></help> <expand macro="citations"/> </tool>