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comparison phylogenomics_analysis.xml @ 39:53f404994667 draft

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author greg
date Fri, 27 Jan 2017 15:03:32 -0500
parents 5423ad5c4f00
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38:5423ad5c4f00 39:53f404994667
1 <tool id="plant_tribes_phylogenomics_analysis" name="PhylogenomicsAnalysis" version="1.0.0"> 1 <tool id="plant_tribes_phylogenomics_analysis" name="Perform phylogenomic analyses" version="0.3">
2 <description>pipeline</description> 2 <description>by creating multiple sequence alignments and inferred maximum likelihood phylogenies</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.2">plant_tribes_phylogenomics_analysis</requirement> 4 <requirement type="package" version="0.3">plant_tribes_phylogenomics_analysis</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <!-- Anything other than zero is an error --> 7 <!-- Anything other than zero is an error -->
8 <exit_code range="1:" /> 8 <exit_code range="1:" />
9 <!-- In case the return code has not been set properly check stderr too --> 9 <!-- In case the return code has not been set properly check stderr too -->
184 <option value="yes">Yes</option> 184 <option value="yes">Yes</option>
185 </param> 185 </param>
186 <when value="no" /> 186 <when value="no" />
187 <when value="yes"> 187 <when value="yes">
188 <conditional name="multiple_sequence_alignments_option_cond"> 188 <conditional name="multiple_sequence_alignments_option_cond">
189 <param name="multiple_sequence_alignments_option" label="Select process for multiple sequence alignments" type="select" force_select="True"> 189 <param name="multiple_sequence_alignments_option" label="Select method for multiple sequence alignments" type="select" force_select="True">
190 <option value="create_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (MAFFT algorithm)</option> 190 <option value="create_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (MAFFT algorithm)</option>
191 <option value="add_alignments">Add unaligned orthogroup proteins to scaffold backbone multiple sequence alignments (MAFFT algorithm)</option> 191 <option value="add_alignments">Add unaligned orthogroup proteins to scaffold backbone multiple sequence alignments (MAFFT algorithm)</option>
192 <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option> 192 <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option>
193 </param> 193 </param>
194 <when value="create_alignments"/> 194 <when value="create_alignments"/>
306 </test> 306 </test>
307 </tests> 307 </tests>
308 <help> 308 <help>
309 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of 309 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
310 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs phylogenomic 310 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs phylogenomic
311 analyses, comparing and analyzing the sequences of single genes, or a small number of genes, as well as many other types of data. 311 analyses by creating multiple sequence alignments and inferred maximum likelihood phylogenies for orthogroups produces by the
312 **Classify gene sequences into precomputed orthologous gene family clusters** tool.
312 313
313 ----- 314 -----
314 315
315 **Options** 316 **Options**
316 317
317 * **Required options** 318 * **Required options**
318 319
319 - **Select sequences classified into gene family clusters** - A history item with the label 'Sequences classified into gene family clusters on...'. 320 - **Select sequences classified into gene family clusters** - A history item with the label 'Sequences classified into gene family clusters on...'.
320 - **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data. 321 - **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
321 - **Protein clustering method** - One of GFam, OrthoFinder or OrthoMCL. 322 - **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
322 323
323 * **Multiple sequence alignments options** 324 * **Multiple sequence alignments options**
324 325
325 - **Select process for multiple sequence alignments** - Process used for setting multiple sequence alignments. 326 - **Select method for multiple sequence alignments** - Method used for setting multiple sequence alignments.
326 - **Input sequences include corresponding coding sequences?** - Selecting 'Yes' for this option requires that 'Yes' was selected for the 'Create orthogroup fasta files?' option on the GeneFamilyClassifier tool when generating the selected input. This tool will produce an error if 'No' was selected. 327 - **Input sequences include corresponding coding sequences?** - Selecting 'Yes' for this option requires that 'Yes' was selected for the 'Create orthogroup fasta files?' option on the 'Classify gene sequences into precomputed orthologous gene family clusters' tool when generating the selected input. This tool will produce an error if 'No' was selected.
327 - **Construct orthogroup multiple codon alignments?** - Construct orthogroup multiple codon alignments. 328 - **Construct orthogroup multiple codon alignments?** - Construct orthogroup multiple codon alignments.
328 - **Sequence type used in the phylogenetic inference** - Sequence type used in the phylogenetic inference. 329 - **Sequence type used in the phylogenetic inference** - Sequence type (dna or amino acid) used in the phylogenetic inference.
329 - **Use corresponding coding sequences?** - Selecting 'Yes' for this option requires that 'Yes' was selected for the 'Create corresponding coding sequences?' option on the GeneFamilyClassifier tool when generating the selected input. This tool will produce an error if 'No' was selected. 330 - **Use corresponding coding sequences?** - Selecting 'Yes' for this option requires that 'Yes' was selected for the 'Create corresponding coding sequences?' option on the 'Classify gene sequences into precomputed orthologous gene family clusters' tool when generating the selected input. This tool will produce an error if 'No' was selected.
330 331
331 * **Phylogenetic trees options** 332 * **Phylogenetic trees options**
332 333
333 - **Phylogenetic trees inference method** - Phylogenetic trees inference method. 334 - **Phylogenetic trees inference method** - Phylogenetic trees inference method.
334 - **Select history item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees?** - If 'No' is selected, trees will be rooted using the most distant taxon present in the orthogroup. 335 - **Select history item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees?** - If 'No' is selected, trees will be rooted using the most distant taxon present in the orthogroup.
335 - **History item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees** -History item containing a set of string fragments matching sequences identifiers of species in the classification (including scaffold taxa) to be used for determining the most basal taxa in the orthogroups for rooting trees. The set of string fragments must be listed in decreasing order from older to younger lineages. 336 - **History item containing strings matching sequence identifiers of species for determining the most basal taxa in the orthogroups for rooting trees** - History item containing a set of string fragments matching sequences identifiers of species in the classification (including scaffold taxa) to be used for determining the most basal taxa in the orthogroups for rooting trees. The set of string fragments must be listed in decreasing order from older to younger lineages.
336 - **Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree** - Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree. 337 - **Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree** - Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree.
337 - **Maximum number of sequences in orthogroup alignments** - Maximum number of sequences in orthogroup alignments. 338 - **Maximum number of sequences in orthogroup alignments** - Maximum number of sequences in orthogroup alignments.
338 - **Minimum number of sequences in orthogroup alignments** - Minimum number of sequences in orthogroup alignments. 339 - **Minimum number of sequences in orthogroup alignments** - Minimum number of sequences in orthogroup alignments.
339 340
340 * **MSA quality control options** 341 * **MSA quality control options**
345 346
346 </help> 347 </help>
347 <citations> 348 <citations>
348 <citation type="bibtex"> 349 <citation type="bibtex">
349 @unpublished{None, 350 @unpublished{None,
350 author = {None}, 351 author = {Eric Wafula},
351 title = {None}, 352 title = {None},
352 year = {None}, 353 year = {None},
353 eprint = {None}, 354 eprint = {None},
354 url = {None} 355 url = {None}
355 }</citation> 356 }</citation>