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comparison raxml.xml @ 2:6f7ff8a3bd79 draft

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planemo upload for repository https://github.com/stamatak/standard-RAxML commit bcfc8451fa622a6bf3aa31fa1e308c394feefb38
author iuc
date Mon, 14 Nov 2016 13:11:14 -0500
parents 934206441123
children 58a0f16c950c
comparison
equal deleted inserted replaced
1:b0d6eb76ad87 2:6f7ff8a3bd79
1 <tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="1.0.1"> 1 <tool id="raxml" name="Phyogenetic reconstruction with RaXML" version="1.0.2">
2 <description>- Maximum Likelihood based inference of large phylogenetic trees</description> 2 <description>- Maximum Likelihood based inference of large phylogenetic trees</description>
3 <requirements> 3 <requirements>
4 <requirement type='package' version="8.2.4">raxml</requirement> 4 <requirement type='package' version="8.2.4">raxml</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python">raxml.py 6 <command interpreter="python">raxml.py
176 </param> 176 </param>
177 <when value="nucleotide"> 177 <when value="nucleotide">
178 <param name="base_model" type="select" label="Substitution Model" help="--base-model"> 178 <param name="base_model" type="select" label="Substitution Model" help="--base-model">
179 <option value="GTRCAT">GTRCAT</option> 179 <option value="GTRCAT">GTRCAT</option>
180 <option value="GTRCATI">GTRCATI</option> 180 <option value="GTRCATI">GTRCATI</option>
181 <option value="GTRGAMMA" select="true">GTRGAMMA</option> 181 <option value="GTRGAMMA" selected="true">GTRGAMMA</option>
182 <option value="GTRGAMMAI">GTRGAMMAI</option> 182 <option value="GTRGAMMAI">GTRGAMMAI</option>
183 </param> 183 </param>
184 </when> 184 </when>
185 <when value="aminoacid"> 185 <when value="aminoacid">
186 <param name="aa_model_empirical_base_frequencies" 186 <param name="aa_model_empirical_base_frequencies"
187 type="boolean" checked="no" truevalue="--aa_empirical_freq" falsevalue="" display="checkboxes" label="Use empirical base frequencies in AA models" /> 187 type="boolean" checked="no" truevalue="--aa_empirical_freq" falsevalue="" display="checkboxes" label="Use empirical base frequencies in AA models" />
188 <param name="base_model" type="select" label="Substitution Model (--base_model)"> 188 <param name="base_model" type="select" label="Substitution Model (--base_model)">
189 <option value="PROTCAT" select="true">PROTCAT</option> 189 <option value="PROTCAT" selected="true">PROTCAT</option>
190 <option value="PROTCATI">PROTCATI</option> 190 <option value="PROTCATI">PROTCATI</option>
191 <option value="PROTGAMMA">PROTGAMMA</option> 191 <option value="PROTGAMMA">PROTGAMMA</option>
192 <option value="PROTGAMMAI">PROTGAMMAI</option> 192 <option value="PROTGAMMAI">PROTGAMMAI</option>
193 </param> 193 </param>
194 <param name="aa_search_matrix" type="select" label="Matrix" help="(--aa_search_matrix)"> 194 <param name="aa_search_matrix" type="select" label="Matrix" help="(--aa_search_matrix)">
195 <option value="DAYHOFF" select="true">DAYHOFF</option> 195 <option value="DAYHOFF" selected="true">DAYHOFF</option>
196 <option value="DCMUT">DCMUT</option> 196 <option value="DCMUT">DCMUT</option>
197 <option value="JTT">JTT</option> 197 <option value="JTT">JTT</option>
198 <option value="MTREV">MTREV</option> 198 <option value="MTREV">MTREV</option>
199 <option value="WAG">WAG</option> 199 <option value="WAG">WAG</option>
200 <option value="RTREV">RTREV</option> 200 <option value="RTREV">RTREV</option>