Mercurial > repos > iuc > hyphy_busted
comparison macros.xml @ 35:e908c4003bd8 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
| author | iuc |
|---|---|
| date | Thu, 02 Mar 2023 15:18:01 +0000 |
| parents | e931e69b5a80 |
| children |
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| 34:caf23deba39a | 35:e908c4003bd8 |
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| 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[ |