Mercurial > repos > greg > phylogenomics_analysis

comparison phylogenomics_analysis.xml @ 69:34dcfb570551 draft

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author greg
date Thu, 02 Mar 2017 10:08:10 -0500
parents 43252277cb23
children bd26a18387ae
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68:5f76ffe55d0f 69:34dcfb570551
11 <regex match="Error:" /> 11 <regex match="Error:" />
12 <regex match="Exception:" /> 12 <regex match="Exception:" />
13 </stdio> 13 </stdio>
14 <command> 14 <command>
15 <![CDATA[ 15 <![CDATA[
16 #import os
17 #import sys
18
19 #if str($options_type.options_type_selector) == 'advanced': 16 #if str($options_type.options_type_selector) == 'advanced':
20 #set multiple_sequence_alignments_cond = $options_type.multiple_sequence_alignments_cond 17 #set multiple_sequence_alignments_cond = $options_type.multiple_sequence_alignments_cond
21 #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments 18 #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments
22 #if str($multiple_sequence_alignments) == 'yes': 19 #if str($multiple_sequence_alignments) == 'yes':
23 #set multiple_sequence_alignments_option_cond = $options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond 20 #set multiple_sequence_alignments_option_cond = $options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond
267 264
268 ----- 265 -----
269 266
270 **Options** 267 **Options**
271 268
272 * **Required options** 269 * **Required**
273 270
274 - **Select gene family clusters** - Sequences classified into gene family clusters, optionally including corresponding coding sequences. 271 - **Select gene family clusters** - Sequences classified into gene family clusters, optionally including corresponding coding sequences.
275 - **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data. 272 - **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
276 - **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters). 273 - **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
277 274
278 * **Multiple sequence alignments options** 275 * **Multiple sequence alignments**
279 276
280 - **Select method for multiple sequence alignments** - Method used for setting multiple sequence alignments. 277 - **Select method for multiple sequence alignments** - Method used for setting multiple sequence alignments.
281 - **Input sequences include corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptorthocs'. 278 - **Input sequences include corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptorthocs'.
282 - **Construct orthogroup multiple codon alignments?** - Construct orthogroup multiple codon alignments. 279 - **Construct orthogroup multiple codon alignments?** - Construct orthogroup multiple codon alignments.
283 - **Sequence type used in the phylogenetic inference** - Sequence type (dna or amino acid) used in the phylogenetic inference. 280 - **Sequence type used in the phylogenetic inference** - Sequence type (dna or amino acid) used in the phylogenetic inference.
284 - **Use corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptorthocs' or this tool will produce an error. 281 - **Use corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptorthocs' or this tool will produce an error.
285 282
286 * **Phylogenetic trees options** 283 * **Phylogenetic trees**
287 284
288 - **Phylogenetic trees inference method** - Phylogenetic trees inference method. 285 - **Phylogenetic trees inference method** - Phylogenetic trees inference method.
289 - **Select rooting order configuration for rooting trees??** - If 'No' is selected, trees will be rooted using the most distant taxon present in the orthogroup. 286 - **Select rooting order configuration for rooting trees??** - If 'No' is selected, trees will be rooted using the most distant taxon present in the orthogroup.
290 - **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. 287 - **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.
291 - **Maximum number of sequences in orthogroup alignments** - Maximum number of sequences in orthogroup alignments. 288 - **Maximum number of sequences in orthogroup alignments** - Maximum number of sequences in orthogroup alignments.
292 - **Minimum number of sequences in orthogroup alignments** - Minimum number of sequences in orthogroup alignments. 289 - **Minimum number of sequences in orthogroup alignments** - Minimum number of sequences in orthogroup alignments.
293 290
294 * **MSA quality control options** 291 * **MSA quality control**
295 292
296 - **Remove sequences with gaps of** - Removes gappy sequences in alignments (i.e., 0.5 removes sequences with 50% gaps). 293 - **Remove sequences with gaps of** - Removes gappy sequences in alignments (i.e., 0.5 removes sequences with 50% gaps).
297 - **Select process used for gap trimming** - Either nucleotide based trimming or alignments are trimed using using trimAl's ML heuristic trimming approach. 294 - **Select process used for gap trimming** - Either nucleotide based trimming or alignments are trimed using using trimAl's ML heuristic trimming approach.
298 - **Remove sites in alignments with gaps of** - If the process used for gap trimming is nucleotide based, this is the gap value used when removing gappy sites in alignments (i.e., 0.1 removes sites with 90% gaps). 295 - **Remove sites in alignments with gaps of** - If the process used for gap trimming is nucleotide based, this is the gap value used when removing gappy sites in alignments (i.e., 0.1 removes sites with 90% gaps).
299 296