Partitionfinder2 REST

PartitionFinder2 XSEDE interface:

This interface is used from the REST API to convey input files, and configure the command line PartitionFinder2 parameters. .

The Tool ID for this interface is toolId=partitionfinder2_xsede

Supported parameters: Input files:
input.infile_= - Primary Input File
input.supply_usertreetop_= (InFile) - Use a tree file in Newick format
input.cfg_select_= (InFile) Select cgf file (If you provide a.cfg file, you please be sure it specifies alignment=infile.phy)

Supported parameters:
vparam.runtime_= (Float) Maximum Hours to Run (up to 168 hours) default=0.5
vparam.datatype_= (Excl) default=DNA; Protein, Morphology
vparam.num_processes_ = (Excl) default = 8. (8,6,4,2,1) Set the number of processes. Decrease when you get an Out Of Memory error. 
vparam.chk_only_= (Switch) Just check the config file default=0
vparam.show_pyexceptions_= (Switch) If errors occur, print the python exceptions default=0
vparam.run_quick_= (Switch) Avoid anything slow (default=0)
vparam.use_raxml_= (Switch) Use RAxML (rather than PhyML, -r). default=0
vparam.use_tiger_= (Switch) Use kmeans=tiger (morphological data only) default=0
vparam.rcluster_max_= (Integer) Number of possible schemes that the relaxed clustering algorithm will consider. The default is to look at the larger value out of 1000, and 10 times the number of data blocks you have.
vparam.min_subset_= (Integer) Minimum subset size that the kmeans and rcluster algorithm will accept ( default=100)
vparam.debug_option_= (String) Provide comma-separated debug regions to output extra information about what the program is doing.
vparam.all_states_= (switch) PartitionFinder should not produce subsets that do not have all possible states present (--all-states)
vparam.branch_lengths_= (Excl)  Linked branch lengths? (linked, unlinked)
vparam.models_choice_= (Excl) Select the model (when no cfg file selected)  (all, allx, beast, mrbayes, gamma, gammai)
vparam.models_choicestring_= (Switch) Specify a model list
vparam.models_choice2_= (string) Enter the model list
vparam.model_selection_= (Excl) Select the metric for model (model_selection) when no cfg selected. (aic, aicc, bic)
vparam.search_choice_= (Excl) Select the search algorithm (all, greedy, rcluster, rclusterf, hcluster, kmeans) when cfg file not slected
vparam.num_datablocks_= (Inteer) How many datablocks do you have? <= 10
  
when $num_datablocks >= 1
vparam.datablock_1a_= (String) Enter the name of your tenth datablock
vparam.datablock1_range1_= (Integer) Enter the beginning of the range
vparam.datablock1_range2_= (Integer) Enter the end of the range
vparam.datablock1_codon_= (Switch)  This a codon analysis (will repeat the range /1,/2, and /3)

when $num_datablocks >= 2
vparam.datablock_2a_ = (String) Enter the name of your tenth datablock
vparam.datablock2_range1_= (Integer) Enter the beginning of the range
vparam.datablock2_range2_= (Integer) Enter the end of the range
vparam.datablock2_codon_= (Switch)  This a codon analysis (will repeat the range /1,/2, and /3)

when $num_datablocks >= 3
vparam.datablock_3a_= (String) Enter the name of your tenth datablock
vparam.datablock3_range1_= (Integer) Enter the beginning of the range
vparam.datablock3_range2_= (Integer) Enter the end of the range
vparam.datablock3_codon_= (Switch)  This a codon analysis (will repeat the range /1,/2, and /3)

when $num_datablocks >= 4
vparam.datablock_4a_= (String) Enter the name of your tenth datablock
vparam.datablock4_range1_= (Integer) Enter the beginning of the range
vparam.datablock4_range2_= (Integer) Enter the end of the range
vparam.datablock4_codon_= (Switch)  This a codon analysis (will repeat the range /1,/2, and /3)

when $num_datablocks >= 5
vparam.datablock_5a_= (String) Enter the name of your tenth datablock
vparam.datablock5_range1_= (Integer) Enter the beginning of the range
vparam.datablock5_range2_= (Integer) Enter the end of the range
vparam.datablock5_codon_= (Switch)  This a codon analysis (will repeat the range /1,/2, and /3)

when $num_datablocks >= 6
vparam.datablock_6a_= (String) Enter the name of your tenth datablock
vparam.datablock6_range1_= (Integer) Enter the beginning of the range
vparam.datablock6_range2_= (Integer) Enter the end of the range
vparam.datablock6_codon_= (Switch)  This a codon analysis (will repeat the range /1,/2, and /3)

when $num_datablocks6 >= 7
vparam.datablock_7a_= (String) Enter the name of your tenth datablock
vparam.datablock7_range1_= (Integer) Enter the beginning of the range
vparam.datablock7_range2_= (Integer) Enter the end of the range
vparam.datablock7_codon_= (Switch)  This a codon analysis (will repeat the range /1,/2, and /3)

when $num_datablocks >= 8
vparam.datablock_8a_= (String) Enter the name of your tenth datablock
vparam.datablock8_range1_= (Integer) Enter the beginning of the range
vparam.datablock8_range2_= (Integer) Enter the end of the range
vparam.datablock8_codon_= (Switch)  This a codon analysis (will repeat the range /1,/2, and /3)
  
when $num_datablocks >= 9
vparam.datablock_9a_= (String) Enter the name of your tenth datablock
vparam.datablock9_range1_= (Integer) Enter the beginning of the range
vparam.datablock9_range2_= (Integer) Enter the end of the range
vparam.datablock9_codon_= (Switch)  This a codon analysis (will repeat the range /1,/2, and /3)
  
when $num_datablocks >= 10
vparam.datablock_10a_= (String) Enter the name of your tenth datablock
vparam.datablock10_range1_= (Integer) Enter the beginning of the range
vparam.datablock10_range2_= (Integer) Enter the end of the range
vparam.datablock10_codon_= (switch)  This a codon analysis (will repeat the range /1,/2, and /3)
 

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