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comparison qiime2/qiime_phylogeny_iqtree-ultrafast-bootstrap.xml @ 4:71f124e02000 draft default tip

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Fixes
author florianbegusch
date Tue, 13 Aug 2019 07:40:25 -0400
parents 149432539226
children
comparison
equal deleted inserted replaced
3:eda5df31da55 4:71f124e02000
11 11
12 #if str($pseed): 12 #if str($pseed):
13 --p-seed="$pseed" 13 --p-seed="$pseed"
14 #end if 14 #end if
15 15
16 #if $pncores: 16
17 --p-n-cores=$pncores 17 #set $pncores = '${GALAXY_SLOTS:-4}'
18 #end if 18 #if str($pncores):
19 19 --p-n-cores=$pncores
20 #if $pnruns: 20 #end if
21
22
23 #if str($pnruns):
21 --p-n-runs=$pnruns 24 --p-n-runs=$pnruns
22 #end if 25 #end if
23 26
24 #if str($psubstitutionmodel) != 'None': 27 #if str($psubstitutionmodel) != 'None':
25 --p-substitution-model=$psubstitutionmodel 28 --p-substitution-model=$psubstitutionmodel
26 #end if 29 #end if
27 30
28 #if $pbootstrapreplicates: 31 #if str($pbootstrapreplicates):
29 --p-bootstrap-replicates=$pbootstrapreplicates 32 --p-bootstrap-replicates=$pbootstrapreplicates
30 #end if 33 #end if
31 34
32 #if str($pninitparstrees): 35 #if str($pninitparstrees):
33 --p-n-init-pars-trees="$pninitparstrees" 36 --p-n-init-pars-trees="$pninitparstrees"
98 cp otree.qza $otree 101 cp otree.qza $otree
99 ]]></command> 102 ]]></command>
100 <inputs> 103 <inputs>
101 <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] Aligned sequences to be used for phylogenetic reconstruction. [required]" name="ialignment" optional="False" type="data"/> 104 <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] Aligned sequences to be used for phylogenetic reconstruction. [required]" name="ialignment" optional="False" type="data"/>
102 <param label="--p-seed: INTEGER Random number seed. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pseed" optional="True" type="integer"/> 105 <param label="--p-seed: INTEGER Random number seed. If not set, program defaults will be used. See IQ-TREE manual for details. [optional]" name="pseed" optional="True" type="integer"/>
103 <param label="--p-n-cores: INTEGER The number of cores to use for parallel processing. Range(0, None) Use '0' to let IQ-TREE automatically determine the optimal number of cores to use. [default: 1]" name="pncores" optional="True" type="integer" min="0" value="1"/>
104 <param label="--p-n-runs: INTEGER Number of indepedent runs. Multiple independent Range(1, None) runs (e.g. 10) can outperform a single run in terms of likelihood maximisation. [default: 1]" name="pnruns" optional="True" type="integer" min="1" value="1"/> 106 <param label="--p-n-runs: INTEGER Number of indepedent runs. Multiple independent Range(1, None) runs (e.g. 10) can outperform a single run in terms of likelihood maximisation. [default: 1]" name="pnruns" optional="True" type="integer" min="1" value="1"/>
105 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select"> 107 <param label="--p-substitution-model: " name="psubstitutionmodel" optional="True" type="select">
106 <option selected="True" value="None">Selection is Optional</option> 108 <option selected="True" value="None">Selection is Optional</option>
107 <option value="JC">JC</option> 109 <option value="JC">JC</option>
108 <option value="JC+I">JC+I</option> 110 <option value="JC+I">JC+I</option>