Mercurial > repos > iuc > mothur_dist_seqs
diff dist.seqs.xml @ 4:2211f97b6d1b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:49:49 -0500 |
| parents | 699ed9de9edf |
| children | 3456fb5f8a3a |
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--- a/dist.seqs.xml Tue Sep 05 16:05:25 2017 -0400 +++ b/dist.seqs.xml Wed Feb 14 09:49:49 2018 -0500 @@ -7,28 +7,28 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$fasta" fasta.dat && +## create symlinks to input datasets +ln -s '$fasta' fasta.dat && - echo 'dist.seqs( - fasta=fasta.dat, - #if $calc: - calc=$calc, - #end if - countends=$countends, - #if $cutoff: - cutoff=$cutoff, - #end if - #if $output: - output=$output, - #end if - processors='\${GALAXY_SLOTS:-8}' - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'dist.seqs( + fasta=fasta.dat, + #if $calc: + calc=$calc, + #end if + countends=$countends, + #if $cutoff: + cutoff=$cutoff, + #end if + #if $output: + output=$output, + #end if + 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,fasta" label="fasta - Alignment Fasta"/> @@ -39,7 +39,8 @@ <option value="eachgap ">eachgap - penalize each gap</option> </param> <param name="countends" type="boolean" checked="true" truevalue="true" falsevalue="false" label="countends - Penalize terminal gaps"/> - <param name="cutoff" type="float" value="" min="0.0" optional="true" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Do not save any distances larger than this, a common value would be 0.10"/> + <param name="cutoff" type="float" value="" min="0.0" optional="true" label="cutoff - Distance Cutoff threshold - ignored if not > 0" + help="Do not save any distances larger than this, a common value would be 0.10"/> <param name="output" type="select" label="output - Distance Matrix Output Format" help=""> <option value="" selected="true">Default Column-Formatted Matrix</option> <option value="lt">Phylip formatted Lower Triangle Matrix</option> @@ -71,8 +72,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -86,7 +86,6 @@ v.1.20.0: Updated to Mothur 1.33 -]]> - </help> + ]]></help> <expand macro="citations"/> </tool>