Mercurial > repos > tiagoantao > raxml
diff raxml.xml @ 20:d930ea30718d draft
planemo upload commit ed695dda2a4744fbe43dccf521d4de7a57c85501
| author | tiagoantao |
|---|---|
| date | Tue, 03 Nov 2015 15:44:56 -0500 |
| parents | 2c55b607264c |
| children | 48526baa210f |
line wrap: on
line diff
--- a/raxml.xml Mon Nov 02 16:16:02 2015 -0500 +++ b/raxml.xml Tue Nov 03 15:44:56 2015 -0500 @@ -16,9 +16,7 @@ --model_type $search_model_selector.model_type --base_model $search_model_selector.base_model #if str( $search_model_selector.model_type ) == 'aminoacid': - #if str( $search_model_selector.aa_model_empirical_base_frequences) == 'true': - --aa_empirical_freq - #end if + $search_model_selector.aa_model_empirical_base_frequencies #if $search_model_selector.aa_search_matrix: --aa_search_matrix $search_model_selector.aa_search_matrix #end if @@ -57,13 +55,9 @@ --numofcats $selExtraOpts.numofcats #end if ## (-d) - #if str ($selExtraOpts.search_complete_random_tree) == "true": - --search_complete_random_tree - #end if + $selExtraOpts.search_complete_random_tree ## (-D) - #if str ($selExtraOpts.ml_search_convergence) == "true": - --ml_search_convergence - #end if + $selExtraOpts.ml_search_convergence) ## (-e) #if $selExtraOpts.model_opt_precision: --model_opt_precision $selExtraOpts.model_opt_precision @@ -77,9 +71,7 @@ --search_algorithm $selExtraOpts.search_algorithm #end if ## (-F) - #if str ($selExtraOpts.save_memory_cat_model) == "true": - --save_memory_cat_model - #end if + $selExtraOpts.save_memory_cat_model ## (-g) #if $selExtraOpts.groupingfile: --groupingfile $selExtraOpts.groupingfile @@ -101,27 +93,21 @@ --majority_rule_consensus $selExtraOpts.majority_rule_consensus #end if ## (-k) - #if str ($selExtraOpts.print_branch_lengths) == "true": - --print_branch_lengths - #end if + $selExtraOpts.print_branch_lengths ## (-K) #if str ($selExtraOpts.multistate_sub_model) != "": --multistate_sub_model $selExtraOpts.multistate_sub_model #end if ## (-m) - see elsewhere ## (-M) - #if str ($selExtraOpts.estimate_individual_branch_lengths) == "true": - --estimate_individual_branch_lengths - #end if + $selExtraOpts.estimate_individual_branch_lengths ## (-n) - see elsewhere ## (-o) #if $selExtraOpts.outgroup_name: --outgroup_name $selExtraOpts.outgroup_name #end if ## (-O) - #if str ($selExtraOpts.disable_undetermined_seq_check) == "true": - --disable_undetermined_seq_check - #end if + $selExtraOpts.disable_undetermined_seq_check ## (-P) #if $selExtraOpts.external_protein_model: --external_protein_model $selExtraOpts.external_protein_model @@ -152,13 +138,9 @@ --use_median_approximation #end if ## (-U) - #if str ($selExtraOpts.save_memory_gappy_alignments) == "true": - --save_memory_gappy_alignments - #end if + $selExtraOpts.save_memory_gappy_alignments ## (-V) - #if str ($selExtraOpts.disable_rate_heterogeneity) == "true": - --disable_rate_heterogeneity - #end if + $selExtraOpts.disable_rate_heterogeneity ## (-W) #if $selExtraOpts.sliding_window_size: --sliding_window_size $selExtraOpts.sliding_window_size @@ -168,34 +150,17 @@ --rapid_bootstrap_random_seed $selExtraOpts.rapid_bootstrap_random_seed #end if ## (-y) - #if str ($selExtraOpts.parsimony_starting_tree_only) == "true": - --parsimony_starting_tree_only - #end if + $selExtraOpts.parsimony_starting_tree_only) ## (-z) #if $selExtraOpts.file_multiple_trees: --file_multiple_trees $selExtraOpts.file_multiple_trees #end if #end if -##silent sys.stderr.write("DEBUG1 START\n") -##silent sys.stderr.write($selExtraOpts.extraOptions) -##silent sys.stderr.write("\nDEBUG1 END\n") - </command> <inputs> - <conditional name="choose_input_type"> - <param name="input_type" type="select" label="Input type"> - <option value="fasta">Fasta</option> - <option value="phylip">Phylip</option> - </param> - ## (-s) - <when value="fasta"> - <param type="data" format="fasta" name="infile" label="Source file"/> - </when> - <when value="phylip"> - <param type="data" format="phylip" name="infile" label="Source file"/> - </when> - </conditional> + ## (-s) + <param type="data" format="fasta,phylip" name="infile" label="Source file"/> ## (-m) <conditional name="search_model_selector"> <param name="model_type" type="select" label="Model Type"> @@ -206,7 +171,7 @@ </param> <when value="nucleotide"> ## Nucleotide substitution models - <param name="base_model" type="select" label="Substitution Model (-m)"> + <param name="base_model" type="select" label="Substitution Model"> <option value="GTRCAT">GTRCAT</option> <option value="GTRCATI">GTRCATI</option> <option value="GTRGAMMA" select="true">GTRGAMMA</option> @@ -215,8 +180,8 @@ </when> ## Aminoacid substitution models <when value="aminoacid"> - <param name="aa_model_empirical_base_frequences" - type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Use empirical base frequencies in AA models" /> + <param name="aa_model_empirical_base_frequencies" + type="boolean" checked="no" truevalue="--aa_empirical_freq" falsevalue="" display="checkboxes" label="Use empirical base frequencies in AA models" /> <param name="base_model" type="select" label="Substitution Model (-m)"> <option value="PROTCAT" select="true">PROTCAT</option> <option value="PROTCATI">PROTCATI</option> @@ -250,7 +215,7 @@ </when> ## Binary substitution models <when value="binary"> - <param name="base_model" type="select" label="Substitution Model (-m)"> + <param name="base_model" type="select" label="Substitution Model"> <option value="BINCAT">BINCAT</option> <option value="BINCATI">BINCATI</option> <option value="BINGAMMA">BINGAMMA</option> @@ -259,7 +224,7 @@ </when> ## Multi-state substitution models <when value="multistate"> - <param name="base_model" type="select" label="Substitution Model (-m)"> + <param name="base_model" type="select" label="Substitution Model"> <option value="MULTICAT">MULTICAT</option> <option value="MULTICATI">MULTICATI</option> <option value="MULTIGAMMA">MULTIGAMMA</option> @@ -268,7 +233,7 @@ </when> </conditional> <param name="random_seed" type="integer" value="1234567890" size="12" label="Random - seed used for the parsimony inferences (-p)" /> + seed used for the parsimony inferences" /> <conditional name="selExtraOpts"> <param name="extraOptions" type="select" label="RAxML options to use" help="The required minimal settings are the input file and the @@ -279,15 +244,15 @@ <when value="full"> ## (-N/#) <param name="number_of_runs" type="integer" size="8" value="" - label="Number of runs (-N|#)" help="Specify the number of - alternative runs on distinct starting trees In combination + label="Number of runs" help="Specify the number of + alternative runs (-N|#) on distinct starting trees In combination with the '-b' option will invoke a multiple boostrap analysis. You can add the bootstopping criteria by choosing the autoMR, autoMRE, autoMRE_IGN, or autoFC value in a menu below instead of providing a number here. Bootstopping will only work in combination with '-x' or '-b'." optional="True" /> - <param name="number_of_runs_bootstop" type="select" label="Use bootstopping criteria for number of runs (-N/#)" optional="True"> + <param name="number_of_runs_bootstop" type="select" label="Use bootstopping criteria for number of runs" optional="True"> <option value="" selected="yes"></option> <option value="autoMR">autoMR</option> <option value="autoMRE">autoMRE</option> @@ -296,9 +261,9 @@ </param> ## Alphabetical Listing of Advanced Options ## (-a) - <param format="txt" name="weightfile" type="data" label="Column weight file (-a)" optional="True" /> + <param format="txt" name="weightfile" type="data" label="Column weight file" optional="True" /> ## (-A) - <param name="secondary_structure_model" type="select" label="Secondary structure substitution model (-A)" optional="True"> + <param name="secondary_structure_model" type="select" label="Secondary structure substitution model" optional="True"> <option value="" selected="yes"></option> <option value="S6A">S6A</option> <option value="S6B">S6B</option> @@ -316,24 +281,24 @@ <option value="S16B">S16B</option> </param> ## (-b) - <param name="bootseed" type="integer" size="8" value="" label="Random number for non-parametric bootstrapping (-b)" refresh_on_change='true' optional="True" /> + <param name="bootseed" type="integer" size="8" value="" label="Random number for non-parametric bootstrapping" refresh_on_change='true' optional="True" /> ## (-x) - <param name="rapid_bootstrap_random_seed" type="integer" value='' size="7" label="Rapid bootstrapping random seed (-x)" optional="True" help="Specify a random seed and turn on rapid bootstrapping. CAUTION: unlike in version 7.0.4 RAxML will conduct rapid BS replicates under the model of rate heterogeneity you specified via '-m' and not by default under CAT." /> + <param name="rapid_bootstrap_random_seed" type="integer" value='' size="7" label="Rapid bootstrapping random seed" optional="True" help="Specify a random seed and turn on rapid bootstrapping. CAUTION: unlike in version 7.0.4 RAxML will conduct rapid BS replicates under the model of rate heterogeneity you specified via '-m' and not by default under CAT." /> ## (-B) - <param name="cutoff_threshold" type="float" size="8" label="MR Cutoff threshold (-B)" value="" help="Cutoff threshold for the MR-based bootstopping criteria, recommended value is 0.1" optional="True" /> + <param name="cutoff_threshold" type="float" size="8" label="MR Cutoff threshold" value="" help="Cutoff threshold for the MR-based bootstopping criteria, recommended value is 0.1" optional="True" /> ## (-c) - <param name="numofcats" type="integer" size="8" label="Number of Rate Categories for GTRCAT/GTRMIX (-c)" optional="True" /> + <param name="numofcats" type="integer" size="8" label="Number of Rate Categories for GTRCAT/GTRMIX" optional="True" /> ## (-C) Conduct model parameter optimization doesn't work in the pthreads version. Skip for now. ## (-d) - <param name="search_complete_random_tree" type="boolean" checked="False" truevalue="true" falsevalue="false" display="checkboxes" label="Start ML optimization from a complete random starting tree (-d)" /> + <param name="search_complete_random_tree" type="boolean" checked="False" truevalue="--search_complete_random_tree" falsevalue="" display="checkboxes" label="Start ML optimization from a complete random starting tree" /> ## (-D) - <param name="ml_search_convergence" type="boolean" checked="False" truevalue="true" falsevalue="false" label="ML search convergence criterion (-D)" /> + <param name="ml_search_convergence" type="boolean" checked="False" truevalue="--ml_search_convergence" falsevalue="" label="ML search convergence criterion" /> ## (-e) - <param name="model_opt_precision" type="float" size="8" label="Model optimization precision (-e)" value="" help="Set model optimization precision in log likelihood units when MIX/MIXI or GAMMA/GAMMAI models are used" optional="True" /> + <param name="model_opt_precision" type="float" size="8" label="Model optimization precision" value="" help="Set model optimization precision in log likelihood units when MIX/MIXI or GAMMA/GAMMAI models are used" optional="True" /> ## (-E) - <param format="txt" name="excludefile" type="data" label="Exclude file (-E)" optional="True" /> + <param format="txt" name="excludefile" type="data" label="Exclude file" optional="True" /> ## (-f) - <param name="search_algorithm" type="select" label="Algorithm to execute (-f)" optional="True"> + <param name="search_algorithm" type="select" label="Algorithm to execute" optional="True"> <option value="a">Rapid bootstrap and best ML tree search (a)</option> <option value="A">Compute marginal ancestral states (A)</option> <option value="b">Draw bipartition information (b)</option> @@ -361,17 +326,17 @@ <option value="y">Classify environmental sequences into a reference tree (y)</option> </param> ## (-F) - <param name="save_memory_cat_model" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="ML tree searches under CAT model (-F)" optional="True" help="ML tree searches under CAT model for very large trees without switching to GAMMA in the end (saves memory) and no thorough optimization under GAMMA" /> + <param name="save_memory_cat_model" type="boolean" checked="no" truevalue="--save_memory_cat_model" falsevalue="" display="checkboxes" label="ML tree searches under CAT model" optional="True" help="ML tree searches under CAT model for very large trees without switching to GAMMA in the end (saves memory) and no thorough optimization under GAMMA" /> ## (-g) - <param name="groupingfile" format="txt" type="data" label="Multifurcating constraint tree (-g)" optional="True" /> + <param name="groupingfile" format="txt" type="data" label="Multifurcating constraint tree" optional="True" /> ## (-G) - <param name="enable_evol_heuristics" type="float" size="8" label="Enable the ML-based evolutionary placement algorithm heuristics (-G)" help="Enable the ML-based evolutionary placement algorithm heuristics by specifiyng a threshold value (fraction of insertion branches to be evaluated using slow insertions under ML)." optional="True" > + <param name="enable_evol_heuristics" type="float" size="8" label="Enable the ML-based evolutionary placement algorithm heuristics" help="Enable the ML-based evolutionary placement algorithm heuristics by specifiyng a threshold value (fraction of insertion branches to be evaluated using slow insertions under ML)." optional="True" > <validator type="in_range" message="0.0 <= fraction <= 1.0" min="0.0" max="1.0"/> </param> ## (-i) - <param name="initial_rearrangement_setting" type="integer" size="5" value="" label="Initial rearrangement setting (-i)" optional="True" /> + <param name="initial_rearrangement_setting" type="integer" size="5" value="" label="Initial rearrangement setting" optional="True" /> ## (-I) - <param name="posterior_bootstopping_analysis" type="select" label="Posterior bootstopping analysis (-I)" optional="True"> + <param name="posterior_bootstopping_analysis" type="select" label="Posterior bootstopping analysis" optional="True"> <option value="" selected="True"></option> <option value="autoFC">Frequency-based criterion (autoFC)</option> <option value="autoMR">Majority-rule consensus tree criterion (autoMR)</option> @@ -380,7 +345,7 @@ </param> ## (-j) - EMPTY - we cannot handle intermediate tree files in Galaxy ## (-J) - <param name="majority_rule_consensus" type="select" label="Compute consensus tree (-J)" optional="True"> + <param name="majority_rule_consensus" type="select" label="Compute consensus tree" optional="True"> <option value="" selected="True"></option> <option value="MR">Majority-rule consensus tree (MR)</option> <option value="MRE">Extended majority-rule consensus tree (MRE)</option> @@ -389,47 +354,47 @@ <option value="MR_DROP">Identify majority-rule dropsets (MR_DROP)</option> </param> ## (-k) - <param name="print_branch_lengths" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Print bootstrapped trees with branch lengths (-k)" help="Specifies that bootstrapped trees should be printed with branch lengths. The bootstraps will run a bit longer, because model parameters will be optimized at the end of each run under GAMMA or GAMMA+P-Invar respectively." optional="True" /> + <param name="print_branch_lengths" type="boolean" checked="no" truevalue="--print_branch_lengths" falsevalue="" display="checkboxes" label="Print bootstrapped trees with branch lengths" help="Specifies that bootstrapped trees should be printed with branch lengths. The bootstraps will run a bit longer, because model parameters will be optimized at the end of each run under GAMMA or GAMMA+P-Invar respectively." optional="True" /> ## (-K) <param name="multistate_sub_model" type="select" label="Specify a - multi-state substitution model (-K)" optional="True"> + multi-state substitution model" optional="True"> <option value="" selected="true"></option> <option value="GTR">GTR</option> <option value="ORDERED">ORDERED</option> <option value="MK">MK</option> </param> ## (-M) - <param name="estimate_individual_branch_lengths" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Estimate individual per-partition branch lengths (-M)" help="Only has effect with a partition file (-q)." optional="True" /> + <param name="estimate_individual_branch_lengths" type="boolean" checked="no" truevalue="--estimate_individual_branch_lengths" falsevalue="" display="checkboxes" label="Estimate individual per-partition branch lengths" help="Only has effect with a partition file (-q)." optional="True" /> ## (-n) name is hard-coded to 'galaxy' for more straightforward handling of output files ## (-o) - <param name="outgroup_name" type="text" size="40" value="" label="Outgroup name (-o)" help="E.g. Mouse or Mouse,Rat. No spaces between taxon names are allowed." optional="True" /> + <param name="outgroup_name" type="text" size="40" value="" label="Outgroup name" help="E.g. Mouse or Mouse,Rat. No spaces between taxon names are allowed." optional="True" /> ## (-O) - <param name="disable_undetermined_seq_check" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Disable check for completely undetermined sequence in alignment (-O)" optional="True" help="Disable the check for completely undetermined sequence in alignment. The program will not exit with an error message when '-O' is specified." /> - <param name="external_protein_model" format="txt" type="data" label="External AA substitution model (-P)" help="Specify the file name of a user-defined AA (Protein) substitution model. This file must contain 420 entries, the first 400 being the AA substitution rates (this must be a symmetric matrix) and the last 20 are the empirical base frequencies." optional="True" /> + <param name="disable_undetermined_seq_check" type="boolean" checked="no" truevalue="--disable_undertermined_seq_check" falsevalue="" display="checkboxes" label="Disable check for completely undetermined sequence in alignment" optional="True" help="Disable the check for completely undetermined sequence in alignment. The program will not exit with an error message when '-O' is specified." /> + <param name="external_protein_model" format="txt" type="data" label="External AA substitution model" help="Specify the file name of a user-defined AA (Protein) substitution model. This file must contain 420 entries, the first 400 being the AA substitution rates (this must be a symmetric matrix) and the last 20 are the empirical base frequencies." optional="True" /> ## (-q) - <param name="multiple_model" format="txt" type="data" label="Multiple model assignment to alignment partitions (-q)" optional="True" help="Specify the file name which contains the assignment of models to alignment partitions for multiple models of substitution. For the syntax of this file please consult the manual." /> + <param name="multiple_model" format="txt" type="data" label="Multiple model assignment to alignment partitions" optional="True" help="Specify the file name which contains the assignment of models to alignment partitions for multiple models of substitution. For the syntax of this file please consult the manual." /> ## (-r) - <param name="constraint_file" format="txt" type="data" label="Binary constraint tree (-r)" optional="True" help="Specify the file name of a binary constraint tree. This tree does not need to be comprehensive, i.e. must not contain all taxa." /> + <param name="constraint_file" format="txt" type="data" label="Binary constraint tree" optional="True" help="Specify the file name of a binary constraint tree. This tree does not need to be comprehensive, i.e. must not contain all taxa." /> ## (-R) - <param name="bin_model_parameter_file" format="txt" type="data" label="Binary model parameter file (-R)" optional="True" help="Specify the file name of a binary model parameter file that has previously been generated with RAxML using the '-f e' tree evaluation option." /> + <param name="bin_model_parameter_file" format="txt" type="data" label="Binary model parameter file" optional="True" help="Specify the file name of a binary model parameter file that has previously been generated with RAxML using the '-f e' tree evaluation option." /> ## (-s) source file option is in the required options section ## (-S) - <param name="secondary_structure_file" format="txt" type="data" label="Secondary structure file (-S)" optional="True" help="Specify the name of a secondary structure file. The file can contain '.' for alignment columns that do not form part of a stem and characters '()<>[]{}' to define stem regions and pseudoknots."/> + <param name="secondary_structure_file" format="txt" type="data" label="Secondary structure file" optional="True" help="Specify the name of a secondary structure file. The file can contain '.' for alignment columns that do not form part of a stem and characters '()<>[]{}' to define stem regions and pseudoknots."/> ## (-t) - <param name="start_tree_file" format="txt" type="data" label="Starting tree file (-t)" optional="True" help="Specify a user starting tree file name in Newick format." /> + <param name="start_tree_file" format="txt" type="data" label="Starting tree file" optional="True" help="Specify a user starting tree file name in Newick format." /> ## (-T) is hard-coded in the required options section - <param name="use_median_approximation" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Use the median for the discrete approximation (-u)" help="Use the median for the discrete approximation of the GAMMA model of rate heterogeneity." optional="True" /> + <param name="use_median_approximation" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Use the median for the discrete approximation" help="Use the median for the discrete approximation of the GAMMA model of rate heterogeneity." optional="True" /> ## (-U) - <param name="save_memory_gappy_alignments" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Save memory on large gappy alignments (-U)" help="Try to save memory by using SEV-based implementation for gap columns on large gappy alignments." optional="True" /> + <param name="save_memory_gappy_alignments" type="boolean" checked="no" truevalue="--save_memory_gappy_alignments" falsevalue="" display="checkboxes" label="Save memory on large gappy alignments" help="Try to save memory by using SEV-based implementation for gap columns on large gappy alignments." optional="True" /> ## (-V) - <param name="disable_rate_heterogeneity" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Disable rate heterogeneity (-V)" help="Disable rate heterogeneity among sites model and use one without rate heterogeneity instead. Only works if you specify the CAT model of rate heterogeneity." optional="True" /> + <param name="disable_rate_heterogeneity" type="boolean" checked="no" truevalue="--disable_raite_heterogeneity" falsevalue="" display="checkboxes" label="Disable rate heterogeneity" help="Disable rate heterogeneity among sites model and use one without rate heterogeneity instead. Only works if you specify the CAT model of rate heterogeneity." optional="True" /> ## (-W) - <param name="sliding_window_size" type="integer" size="5" value="" label="Sliding window size (-W)" optional="True" help="Sliding window size for leave-one-out site-specific placement bias algorithm. Only effective when used in combination with '-f S'. Default is '100 sites'" /> + <param name="sliding_window_size" type="integer" size="5" value="" label="Sliding window size" optional="True" help="Sliding window size for leave-one-out site-specific placement bias algorithm. Only effective when used in combination with '-f S'. Default is '100 sites'" /> ## (-x) - see it by the (-b) ## (-y) - <param name="parsimony_starting_tree_only" type="boolean" checked="no" truevalue="true" falsevalue="false" display="checkboxes" label="Compute a randomized parsimony starting tree only (-y)" optional="True" help="If you want to only compute a parsimony starting tree with RAxML specify '-y'. The program will exit after computation of the starting tree." /> + <param name="parsimony_starting_tree_only" type="boolean" checked="no" truevalue="--parsimony_starting_tree_only" falsevalue="" display="checkboxes" label="Compute a randomized parsimony starting tree only" optional="True" help="If you want to only compute a parsimony starting tree with RAxML specify '-y'. The program will exit after computation of the starting tree." /> ## (-z) - <param name="file_multiple_trees" format="txt" type="data" label="Multiple trees file (-z)" help="Specify the file name of a file containing multiple trees e.g. from a bootstrap that shall be used to draw bipartition values onto a tree provided with '-t', It can also be used to compute per site log likelihoods in combination with '-f g' and to read a bunch of trees for '-f h', '-f m' and '-f n'." optional="True" /> + <param name="file_multiple_trees" format="txt" type="data" label="Multiple trees file" help="Specify the file name of a file containing multiple trees e.g. from a bootstrap that shall be used to draw bipartition values onto a tree provided with '-t', It can also be used to compute per site log likelihoods in combination with '-f g' and to read a bunch of trees for '-f h', '-f m' and '-f n'." optional="True" /> </when> ## full option list </conditional> ## END $selExtraOpts </inputs>