Mercurial > repos > iuc > mothur_primer_design
diff primer.design.xml @ 3:14ae2ba4a433 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 10:13:04 -0500 |
| parents | 525400c8be71 |
| children | 6d991249c645 |
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--- a/primer.design.xml Tue Sep 05 16:35:13 2017 -0400 +++ b/primer.design.xml Wed Feb 14 10:13:04 2018 -0500 @@ -7,43 +7,43 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$fasta" fasta.dat && - ln -s "$otu" otu.dat && - ln -s "$name" name.dat && - ln -s "$count" count.dat && +## create symlinks to input datasets +ln -s '$fasta' fasta.dat && +ln -s '$otu' otu.dat && +ln -s '$name' name.dat && +ln -s '$count' count.dat && - echo 'primer.design( - fasta=fasta.dat, - list=otu.dat, - #if $label: - label=$label, - #end if - otulabel=$otulabel, - #if $name: - name=name.dat, - #end if - #if $count: - count=count.dat, - #end if - #if $cutoff: - cutoff=$cutoff, - #end if - #if $mintm: - mintm=$mintm, - #end if - #if $maxtm: - maxtm=$maxtm, - #end if - pdiffs=$pdiffs, - length=$length, - processors='\${GALAXY_SLOTS:-8}' - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'primer.design( + fasta=fasta.dat, + list=otu.dat, + #if $label: + label=$label, + #end if + otulabel=$otulabel, + #if $name: + name=name.dat, + #end if + #if $count: + count=count.dat, + #end if + #if $cutoff: + cutoff=$cutoff, + #end if + #if $mintm: + mintm=$mintm, + #end if + #if $maxtm: + maxtm=$maxtm, + #end if + pdiffs=$pdiffs, + length=$length, + processors='\${GALAXY_SLOTS:-8}' +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="fasta" type="data" format="mothur.align" label="fasta - provide aligned fasta file"/> @@ -82,8 +82,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -93,8 +92,7 @@ .. _primer.design: https://www.mothur.org/wiki/Primer.design -]]> - </help> + ]]></help> <citations> <citation type="doi">10.1128/AEM.01541-09</citation> </citations>