Mercurial > repos > iuc > hyphy_meme

comparison macros.xml @ 34:5fd8dc04d6af draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
author iuc
date Thu, 02 Mar 2023 15:17:27 +0000
parents 5d8389d684bf
children
comparison
equal deleted inserted replaced
33:d5d909979314 34:5fd8dc04d6af
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">2.5.36</token> 3 <token name="@TOOL_VERSION@">2.5.47</token>
4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@PROFILE@">21.05</token>
6
4 <xml name="inputs"> 7 <xml name="inputs">
5 <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" help="If the input file type is NEXUS and it includes a valid newick tree, that tree will override an uploaded newick tree" /> 8 <param name="input_file" type="data" format="fasta,fasta.gz,nex" label="Input FASTA or NEXUS file" help="If the input file type is NEXUS and it includes a valid newick tree, that tree will override an uploaded newick tree" />
6 <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file"/> 9 <param name="input_nhx" type="data" format="nhx,newick" optional="true" label="Input newick file"/>
7 </xml> 10 </xml>
8 <xml name="bio_tools"> 11 <xml name="bio_tools">
9 <xrefs> 12 <xrefs>
10 <xref type="bio.tools">HyPhy</xref> 13 <xref type="bio.tools">HyPhy</xref>
11 </xrefs> 14 </xrefs>
12 </xml> 15 </xml>
13 <xml name="substitution"> 16 <xml name="substitution" tokens="argument">
14 <param name="model" type="select" label="Substitution model"> 17 <param argument="@ARGUMENT@" type="select" label="Substitution model">
15 <option value="GTR">GTR - General time reversible 18 <option value="GTR">GTR - General time reversible
16 model</option> 19 model</option>
17 <option value="LG">LG - Generalist empirical model from 20 <option value="LG">LG - Generalist empirical model from
18 Le and Gascuel (2008)</option> 21 Le and Gascuel (2008)</option>
19 <option value="HIVBm">HIVBm - Specialist empirical model 22 <option value="HIVBm">HIVBm - Specialist empirical model
64 #end if 67 #end if
65 </token> 68 </token>
66 69
67 <xml name="mcmc_options"> 70 <xml name="mcmc_options">
68 <param argument="--chains" type="integer" value="5" min="2" max="20" label="Number of MCMC chains" /> 71 <param argument="--chains" type="integer" value="5" min="2" max="20" label="Number of MCMC chains" />
69 <param argument="--chain-length" name="chain_length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain" /> 72 <param argument="--chain-length" type="integer" value="2000000" min="500000" max="50000000" label="Length of each chain" />
70 <param argument="--burn-in" name="samples" type="integer" value="1000000" min="100000" max="1900000" label="Samples to use for burn-in" /> 73 <param argument="--burn-in" name="samples" type="integer" value="1000000" min="100000" max="1900000" label="Samples to use for burn-in" />
71 <param argument="--samples" name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain" /> 74 <param argument="--samples" name="samples_per_chain" type="integer" value="100" min="50" max="1000000" label="Samples to draw from each chain" />
72 </xml> 75 </xml>
73 76
74 <xml name="gencode"> 77 <xml name="gencode">
75 <param name="gencodeid" type="select" label="Genetic code"> 78 <param argument="--code" name="gencodeid" type="select" label="Genetic code">
76 <option value="Universal">Universal code</option> 79 <option value="Universal">Universal code</option>
77 <option value="Vertebrate-mtDNA">Vertebrate mitochondrial DNA 80 <option value="Vertebrate-mtDNA">Vertebrate mitochondrial DNA
78 code</option> 81 code</option>
79 <option value="Yeast-mtDNA">Yeast mitochondrial DNA 82 <option value="Yeast-mtDNA">Yeast mitochondrial DNA
80 code</option> 83 code</option>
117 </conditional> 120 </conditional>
118 </xml> 121 </xml>
119 122
120 <xml name="branches"> 123 <xml name="branches">
121 <conditional name="branch_cond"> 124 <conditional name="branch_cond">
122 <param name="branch_sel" type="select" label="Set of branches to test"> 125 <param argument="--branches" name="branch_sel" type="select" label="Set of branches to test">
123 <option value="All">All branches</option> 126 <option value="All">All branches</option>
124 <option value="Internal">Internal branches</option> 127 <option value="Internal">Internal branches</option>
125 <option value="Leaves">Leaf branches</option> 128 <option value="Leaves">Leaf branches</option>
126 <option value="'Unlabeled-branches'">Unlabeled branches</option> 129 <option value="'Unlabeled-branches'">Unlabeled branches</option>
127 <option value="specify">Enter a branch label</option> 130 <option value="specify">Enter a branch label</option>
150 <requirement type="package" version="@TOOL_VERSION@">hyphy</requirement> 153 <requirement type="package" version="@TOOL_VERSION@">hyphy</requirement>
151 <yield/> 154 <yield/>
152 </requirements> 155 </requirements>
153 </xml> 156 </xml>
154 <xml name="alternative_model_output"> 157 <xml name="alternative_model_output">
155 <data name="alternative_model" format="hyphy_results.json" from_work_dir="alternative_model.json"> 158 <data name="alternative_model" format="nhx" from_work_dir="alternative_model.nhx" label="${tool.name} on ${on_string}: Alternative model">
156 <filter>advanced['save_alternative_model']</filter> 159 <filter>advanced['save_alternative_model']</filter>
157 </data> 160 </data>
158 </xml> 161 </xml>
159 <xml name="resample"> 162 <xml name="resample">
160 <param argument="--resample" type="integer" value="0" min="0" optional="true" label="Perform parametric bootstrap resampling to derive site-level null LRT distributions" help="Warning: This will result in a significantly slower analysis. This parameter specifies the maximum number of replicates per site." /> 163 <param argument="--resample" type="integer" value="0" min="0" optional="true" label="Perform parametric bootstrap resampling to derive site-level null LRT distributions" help="Warning: This will result in a significantly slower analysis. This parameter specifies the maximum number of replicates per site." />
186 --starting-points $advanced.starting_points 189 --starting-points $advanced.starting_points
187 --syn-rates $advanced.syn_rates 190 --syn-rates $advanced.syn_rates
188 --rates $advanced.rates 191 --rates $advanced.rates
189 --srv $advanced.srv 192 --srv $advanced.srv
190 #if $advanced.save_alternative_model: 193 #if $advanced.save_alternative_model:
191 --save-fit alternative_model.json 194 --save-fit alternative_model.nhx
192 #end if 195 #end if
193 #end if 196 #end if
194 ]]></token> 197 ]]></token>
195 <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token> 198 <token name="@HYPHYMPI@">\${GALAXY_MPIRUN:-mpirun -mca orte_tmpdir_base "\${TMPDIR:-.}" -np \${GALAXY_SLOTS:-1}} HYPHYMPI</token>
196 <token name="@ERRORS@"><![CDATA[ 199 <token name="@ERRORS@"><![CDATA[