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sate_ui.xml
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<?xml version="1.0" encoding="UTF-8" ?>
<option-list>
<infile-option name="path" default="" category="mafft">
<help>Path to MAFFT executables</help>
</infile-option>
<infile-option name="path" default="" category="padaligner">
<help>Path to pad_aligner.py executables</help>
</infile-option>
<infile-option name="path" default="" category="fakealigner">
<help>Path to fakealigner file (can be empty)</help>
</infile-option>
<infile-option name="path" default="" category="faketree">
<help>Path to faketree file (can be empty)</help>
</infile-option>
<infile-option name="path" default="" category="randtree">
<help>Path to randtree executable</help>
</infile-option>
<infile-option name="path" default="" category="prank">
<help>Path to PRANK executable</help>
</infile-option>
<infile-option name="path" default="" category="randtree">
<help>Path to randtree executables</help>
</infile-option>
<infile-option name="path" default="" category="raxml">
<help>Path to RAxML</help>
</infile-option>
<string-option name="model" default="" category="raxml">
<help>Substitution model used by RAxML.</help>
</string-option>
<infile-option name="args" default="" category="raxml">
<help>Arguments to be passed to RAxML.</help>
</infile-option>
<infile-option name="path" default="" category="fasttree">
<help>Path to FastTree</help>
</infile-option>
<string-option name="model" default="" category="fasttree">
<help>Substitution model used by FastTree.</help>
</string-option>
<infile-option name="options" default="" category="fasttree">
<help>Options to be passed to FastTree (equivalent of args).</help>
</infile-option>
<infile-option name="args" default="" category="fasttree">
<help>Arguments to be passed to FastTree.</help>
</infile-option>
<infile-option name="path" default="" category="opal">
<help>Path to Opal jar file</help>
</infile-option>
<infile-option name="path" default="" category="clustalw2">
<help>Path to clustalw2 exeutable</help>
</infile-option>
<infile-option name="path" default="" category="muscle">
<help>Path to muscle exeutable</help>
</infile-option>
<infile-option name="path" default="" category="probalign">
<help>Path to ProbalignAligner exeutable</help>
</infile-option>
<outfile-option name="exportconfig" category="commandline">
<help>Export the configuration to the specified file and exit. This is useful if you want to combine several configurations and command line settings into a single configuration file to be used in other analyses.</help>
</outfile-option>
<infile-option name="input" short="i" category="commandline" must-be-valid="True">
<help>input sequence file</help>
</infile-option>
<infile-option name="treefile" short="t" category="commandline">
<help>starting tree file</help>
</infile-option>
<outfile-option name="temporaries" category="commandline">
<help>directory that will be the parent for this job's temporary file</help>
</outfile-option>
<string-option name="job" short="j" default="satejob" category="commandline">
<help>job name</help>
</string-option>
<outfile-option name="timesfile" category="commandline">
<help>optional file that will store the times of events during the SATe run. If the file exists, new lines will be </help>
</outfile-option>
<bool-option name="aligned" short="a" default="False" category="commandline">
<help>If used, then the input file be will treated as aligned for the purposes of the first round of tree inference (the algorithm will start with tree searching on the input before re-aligning). This option only applies if a starting tree is NOT given.</help>
</bool-option>
<bool-option name="raxml_search_after" default="False" category="commandline">
<help>If used, the the completion of the SATe algorithm will be followed by a tree search using RAxML. This can be useful if a very fast and approximate tree estimator is used during the SATe algorithm.</help>
</bool-option>
<bool-option name="two_phase" default="False" category="commandline">
<help>If used, then the program will not perform the SATe algorithm. Instead it will simply call the sequence aligner to align the entire dataset then will call the tree estimator to obtain the tree.</help>
</bool-option>
<bool-option name="untrusted" default="False" category="commandline">
<help>If used, then the data in the input file will be parsed using a more careful procedure. This will generate more helpful error messages, but will use more memory and be slower. If this option is omitted, the error messages resulting from invalid input data will be more cryptic.</help>
</bool-option>
<choice-option name="datatype" short="d" default="DNA" multichoice="False" category="commandline">
<choice value="DNA"></choice>
<choice value="RNA" ></choice>
<choice value="Protein" ></choice>
<help>Specify DNA, RNA, or Protein to indicate what type of data is specified.</help>
</choice-option>
<bool-option name="keeptemp" short="k" default="False" category="commandline">
<help>Keep temporary running files?</help>
</bool-option>
<bool-option name="keepalignmenttemps" default="False" category="commandline">
<help>Keep even the realignment temporary running files (this only has an effect if keeptemp is also selected).</help>
</bool-option>
<bool-option name="multilocus" short="m" default="False" category="commandline">
<help>Analyze multi-locus data?</help>
</bool-option>
<choice-option name="missing" multichoice="False" category="commandline">
<choice value="Ambiguous"></choice>
<choice value="Absent" ></choice>
<help>How to deal with missing data symbols. Specify either "Ambiguous" or "Absent" if the input data contains ?-symbols</help>
</choice-option>
<bool-option name="auto" default="False" category="commandline">
<help>If used, then default values for the max_subproblem_size and tools will be used based on the dataset size. WARNING: using this option can cause SATe to override some of the other options that you have supplied; we recommend that you run this option with --exportconfig to see the exact set of options that will be used in your analysis.</help>
</bool-option>
<int-option name="num_cpus" default="1" min="1" category="sate" subcategory="platform" must-be-valid="True">
<help>The number of processing cores that you would like to assign to SATe. This number should not exceed the number of cores on your machine.</help>
</int-option>
<int-option name="max_mem_mb" default="1024" min="1024" category="sate" subcategory="platform" must-be-valid="True">
<help>The maximum memory available (for the Java heap size when running Java tools)</help>
</int-option>
<string-option name="aligner" default="mafft" category="sate" subcategory="tools">
<help>The name of the alignment program to use for subproblems.</help>
</string-option>
<string-option name="merger" default="muscle" category="sate" subcategory="tools">
<help>The name of the alignment program to use to merge subproblems.</help>
</string-option>
<string-option name="tree_estimator" default="fasttree" category="sate" subcategory="tools">
<help>The name of the tree inference program to use to find trees on fixed alignments.</help>
</string-option>
<choice-option name="break_strategy" default="centroid" multichoice="True" category="sate" subcategory="decomposition">
<choice value="centroid"><help>The edge that comes closest to dividing the tree into two equally sized subtrees (in terms of the number of leaves).</help></choice>
<choice value="longest" ><help>Longest edge in the tree</help></choice>
<help>The method for choosing an edge when bisecting the tree during decomposition</help>
</choice-option>
<int-option name="max_subproblem_size" default="3" category="sate" subcategory="decomposition" min="0">
<help>The maximum size (number of leaves) of subproblems. When a subproblem contains this number of leaves (or fewer), then it will not be decomposed further.</help>
</int-option>
<number-option name="max_subproblem_frac" default="0.5" category="sate" subcategory="decomposition" min="0.0">
<help>The maximum size (number of leaves) of subproblems specified in terms as a proportion of the total number of leaves. When a subproblem contains this number of leaves (or fewer), then it will not be decomposed further.</help>
</number-option>
<bool-option name="start_tree_search_from_current" default="False" category="sate" subcategory="searching">
<help>If selected that the tree from the previous iteration will be given to the tree searching tool as a starting tree.</help>
</bool-option>
<bool-option name="move_to_blind_on_worse_score" default="False" category="sate" subcategory="acceptance">
<help>If True then SATe will move to the blind mode as soon it encounters a tree/alignment pair with a worse score. This is essentially the same as running in blind mode from the beginning, but it does allow one to terminate a run at an interval from the first time the algorithm fails to improve the score.</help>
</bool-option>
<bool-option name="blind_mode_is_final" default="True" category="sate" subcategory="acceptance">
<help>When the blind mode is final, then SATe will never leave blind mode once it is has entered blind mode.</help>
</bool-option>
<duration-option name="blind_after_total_time" default="-1" category="sate" subcategory="acceptance">
<help>Maximum time (in seconds) that SATe will run before switching to blind mode.</help>
</duration-option>
<int-option name="blind_after_total_iter" default="-1" category="sate" subcategory="acceptance">
<help>Maximum number of iterations that SATe will run before switching to blind mode.</help>
</int-option>
<duration-option name="blind_after_time_without_imp" default="-1" category="sate" subcategory="acceptance">
<help>Maximum time (in seconds) that SATe will run without an improvement in likelihood score before switching to blind mode.</help>
</duration-option>
<int-option name="blind_after_iter_without_imp" default="-1" category="sate" subcategory="acceptance">
<help>Maximum number of iterations without an improvement in likelihood score that SATe will run before switching to blind mode.</help>
</int-option>
<duration-option name="time_limit" default="86400.0" category="sate" subcategory="termination">
<help>Maximum time (in seconds) that SATe will continue starting new iterations of realigning and tree searching. If the number is less than 0, then no time limit will be used.</help>
</duration-option>
<int-option name="iter_limit" default="-1" category="sate" subcategory="termination">
<help>The maximum number of iteration that the SATe algorithm will run. If the number is less than 1, then no iteration limit will be used.</help>
</int-option>
<duration-option name="after_blind_time_term_limit" default="-1" category="sate" subcategory="termination">
<help>Maximum time (in seconds) that SATe will continue starting new iterations of realigning and tree searching after SATe has entered blind mode. If the number is less than 0, then no time limit will be used.</help>
</duration-option>
<int-option name="after_blind_iter_term_limit" default="-1" category="sate" subcategory="termination">
<help>The maximum number of iteration that the SATe algorithm will run after SATe has entered blind mode. If the number is less than 1, then no iteration limit will be used.</help>
</int-option>
<duration-option name="time_without_imp_limit" default="-1" category="sate" subcategory="termination">
<help>Maximum time (in seconds) since the last improvement in score that SATe will continue starting new iterations of realigning and tree searching. If the number is less than 0, then no time limit will be used.</help>
</duration-option>
<int-option name="iter_without_imp_limit" default="-1" category="sate" subcategory="termination">
<help>The maximum number of iterations without an improvement in score that the SATe algorithm will run. If the number is less than 1, then no iteration limit will be used.</help>
</int-option>
<duration-option name="after_blind_time_without_imp_limit" default="-1" category="sate" subcategory="termination">
<help>Maximum time (in seconds) since the last improvement in score that SATe will continue starting new iterations of realigning and tree searching after entering BLIND mode. If the number is less than 0, then no time limit will be used.</help>
</duration-option>
<int-option name="after_blind_iter_without_imp_limit" default="1" category="sate" subcategory="termination">
<help>The maximum number of iterations without an improvement in score that the SATe algorithm will run after entering BLIND mode. If the number is less than 1, then no iteration limit will be used.</help>
</int-option>
<outfile-option name="output_directory" short="o" category="sate" subcategory="output">
<help>directory for output files (defaults to input file directory)</help>
</outfile-option>
<bool-option name="return_final_tree_and_alignment" default="False" category="sate" subcategory="output">
<help>Return the tree and alignment pair from the last iteration (otherwise returns the best tree and alignment pair instead)</help>
</bool-option>
</option-list>