Mercurial > repos > iuc > mothur_sort_seqs
diff sort.seqs.xml @ 3:af77b7eda3ce draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:20:25 -0500 |
| parents | 9900cd702dcf |
| children | 805e64a3ef00 |
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--- a/sort.seqs.xml Tue Sep 05 16:26:55 2017 -0400 +++ b/sort.seqs.xml Wed Feb 14 09:20:25 2018 -0500 @@ -7,48 +7,48 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$fasta_in" fasta_in.dat && - ln -s "$qfile_in" qfile_in.dat && - ln -s "$flow_in" flow_in.dat && - ln -s "$name_in" name_in.dat && - ln -s "$group_in" group_in.dat && - ln -s "$tax_in" tax_in.dat && - ln -s "$accnos" accnos.dat && - ln -s "$count" count.dat && +## create symlinks to input datasets +ln -s '$fasta_in' fasta_in.dat && +ln -s '$qfile_in' qfile_in.dat && +ln -s '$flow_in' flow_in.dat && +ln -s '$name_in' name_in.dat && +ln -s '$group_in' group_in.dat && +ln -s '$tax_in' tax_in.dat && +ln -s '$accnos' accnos.dat && +ln -s '$count' count.dat && - echo 'sort.seqs( - #if $fasta_in: - fasta=fasta_in.dat, - #end if - #if $qfile_in: - qfile=qfile_in.dat, - #end if - #if $flow_in: - flow=flow_in.dat, - #end if - #if $name_in: - name=name_in.dat, - #end if - #if $group_in: - group=group_in.dat, - #end if - #if $tax_in: - taxonomy=tax_in.dat, - #end if - #if $accnos: - accnos=accnos.dat, - #end if - #if $count: - count=count.dat, - #end if - large=$large - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'sort.seqs( + #if $fasta_in: + fasta=fasta_in.dat, + #end if + #if $qfile_in: + qfile=qfile_in.dat, + #end if + #if $flow_in: + flow=flow_in.dat, + #end if + #if $name_in: + name=name_in.dat, + #end if + #if $group_in: + group=group_in.dat, + #end if + #if $tax_in: + taxonomy=tax_in.dat, + #end if + #if $accnos: + accnos=accnos.dat, + #end if + #if $count: + count=count.dat, + #end if + large=$large +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - sequences" help="format must be fasta"/> @@ -114,8 +114,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -126,7 +125,6 @@ .. _sort.seqs: https://www.mothur.org/wiki/Sort.seqs -]]> - </help> + ]]></help> <expand macro="citations"/> </tool>