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comparison iqtree.xml @ 16:8a15b044f890 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit fb879119df5cdf56921e5c0559069a36eb052490
author iuc
date Tue, 15 Oct 2024 18:13:53 +0000
parents f4adc3371cac
children 4e7fd03b0a13
comparison
equal deleted inserted replaced
15:f4adc3371cac 16:8a15b044f890
360 $bootstrap_parameters.nonparametric_bootstrap.tbe 360 $bootstrap_parameters.nonparametric_bootstrap.tbe
361 361
362 #if str($miscellaneous_options.fconst) != '' 362 #if str($miscellaneous_options.fconst) != ''
363 -fconst '$miscellaneous_options.fconst' 363 -fconst '$miscellaneous_options.fconst'
364 #end if 364 #end if
365
366 #if str($miscellaneous_options.blmin) != ''
367 -blmin $miscellaneous_options.blmin
368 #end if
369
370 #if str($miscellaneous_options.blmax) != ''
371 -blmax $miscellaneous_options.blmax
372 #end if
373
365 ]]> 374 ]]>
366 </command> 375 </command>
367 <inputs> 376 <inputs>
368 <section name="general_options" expanded="true" title="General options"> 377 <section name="general_options" expanded="true" title="General options">
369 <param argument="-s" type="data" format="txt,fasta,phylip,nex,clustal,msf" optional="true" label="Specify input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format."/> 378 <param argument="-s" type="data" format="txt,fasta,phylip,nex,clustal,msf" optional="true" label="Specify input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format."/>
682 <section name="miscellaneous_options" expanded="False" title="Miscellaneous options"> 691 <section name="miscellaneous_options" expanded="False" title="Miscellaneous options">
683 <param argument="-fconst" type="text" optional="true" label="Specify a list of comma-separated integer numbers" help="The number of entries should be equal to the number of states in the model (e.g. 4 for DNA and 20 for protein). IQ-TREE will then add a number of constant sites accordingly. For example, -fconst 10,20,15,40 will add 10 constant sites of all A, 20 constant sites of all C, 15 constant sites of all G and 40 constant sites of all T into the alignment."> 692 <param argument="-fconst" type="text" optional="true" label="Specify a list of comma-separated integer numbers" help="The number of entries should be equal to the number of states in the model (e.g. 4 for DNA and 20 for protein). IQ-TREE will then add a number of constant sites accordingly. For example, -fconst 10,20,15,40 will add 10 constant sites of all A, 20 constant sites of all C, 15 constant sites of all G and 40 constant sites of all T into the alignment.">
684 <expand macro="sanitize_query" 693 <expand macro="sanitize_query"
685 validinitial="string.digits,string.punctuation" /> 694 validinitial="string.digits,string.punctuation" />
686 </param> 695 </param>
696 <param argument="-blmin" type="float" min="0" max="1" value="" optional="true" label="Specify minimum branch length" help="Default: the smaller of 0.000001 and 0.1/alignment_length." />
697 <param argument="-blmax" type="float" min="0" max="1" value="" optional="true" label="Specify the maximum branch length" help="Default: 10" />
687 </section> 698 </section>
688 </inputs> 699 </inputs>
689 <outputs> 700 <outputs>
690 <data name="bionj" format="nhx" from_work_dir="*.bionj" label="${tool.name} on ${on_string}: BIONJ Tree" /> 701 <data name="bionj" format="nhx" from_work_dir="*.bionj" label="${tool.name} on ${on_string}: BIONJ Tree" />
691 <data name="treefile" format="nhx" from_work_dir="*.treefile" label="${tool.name} on ${on_string}: MaxLikelihood Tree" /> 702 <data name="treefile" format="nhx" from_work_dir="*.treefile" label="${tool.name} on ${on_string}: MaxLikelihood Tree" />