//!@file collection of help texts for command line options
//format: {"option name", "help text"}

{"help", "Print this help."}, {"galaxy_xml", "Print galaxy xml wrapper."},
    {"version", "Print only version string."},
    {"verbose",
     "Be verbose. Prints input parameters, sequences and size information."},
    {"quiet", "Be quiet."},
    {"indel",
     "Indel score. Score contribution of each single base insertion or "
     "deletion. "
     "Indel opening score and indel score define the affine scoring of gaps."},
    {"indel_opening",
     "Indel opening score. Score contribution of opening an insertion or "
     "deletion, "
     "i.e. score for a consecutive run of deletions or insertions. Indel "
     "opening "
     "score and indel score define the affine scoring of gaps."},
    {"ribosum_file",
     "File specifying the Ribosum base and base-pair "
     "similarities. [default: "
     "use RIBOSUM85_60 without requiring a Ribosum file.]"},
    {"use_ribosum",
     "Use ribosum scores for scoring base matches and base pair matches; "
     "note that tau=0 suppresses any effect on the latter."},
    {"ribofit",
     "Use Ribofit base and arc match scores adapted to sequence indentity "
     "(overrides ribosum-file and use-ribosum)."},
    {"match",
     "Set score contribution of a base match (unless ribosum scoring)."},
    {"mismatch",
     "Set score contribution of a base mismatch (unless ribosum scoring)."},
    {"unpaired_penalty", "Penalty for unpaired bases"},
    {"struct_weight",
     "Maximal weight of 1/2 arc match. Balances structure vs. sequence score "
     "contributions."},
    {"exp_prob",
     "Expected base pair probability. Used as background probability for "
     "base pair scoring [default: calculated from sequence length]."},
    {"tau",
     "Tau factor. Factor for contribution of sequence similarity in an arc "
     "match (in percent). tau=0 does not penalize any sequence information "
     "including compensatory mutations at arc matches, while tau=100 "
     "scores sequence similarity at ends of base matches (if a scoring "
     "matrix like ribosum is used, this adds the contributions for "
     "base pair match from the matrix). [default tau=0!]"},
    {"exclusion",
     "Score contribution per exclusion in structure local alignment. Set to "
     "zero for unrestricted structure locality."},
    {"stacking", "Use stacking terms (requires stack-probs by RNAfold -p2)"},
    {"new_stacking",
     "Use new stacking terms (requires stack-probs by RNAfold -p2)"},
    {"struct_local",
     "Turn on/off structure locality. Allow exclusions in alignments of "
     "connected substructures."},
    {"sequ_local",
     "Turn on/off sequence locality. Find best alignment of arbitrary "
     "subsequences of the input sequences."},
    {"free_endgaps",
     "Control where end gaps are allowed for free. "
     "String of four +/- symbols, allowing/disallowing free end "
     "gaps at the four sequence ends "
     "in the order left end of first sequence, right end of first sequence, "
     "left end of second sequence, right end of second sequence. For "
     "example, \"+---\" allows free end gaps at the left end of the first "
     "alignment string; \"----\" forbids free end gaps [default]."},
    {"width", "Width of alignment output."},
    {"clustal", "Write alignment in ClustalW (aln) format to given file."},
    {"stockholm", "Write alignment Stockholm format to given file."},
    {"pp", "Write alignment in PP format to given file."},
    {"alifold_consensus_dp",
     "Compute consensus dot plot by alifold (warning: this may fail for long "
     "sequences)."},
    {"cons_struct_type",
     "Type of consensus structures written to screen and "
     "stockholm output [alifold|mea|none] (default: none)."},
    {"consensus_gamma",
     "Base pair weight for mea consensus computation. For MEA, base pairs are "
     "scored by their pair probability times 2 gamma; unpaired bases, "
     "by their unpaired probability."},
    {"local_output", "Output only local sub-alignment (to std out)."},
    {"local_file_output", "Write only local sub-alignment to output files."},
    {"pos_output", "Output only local sub-alignment positions."},
    {"write_structure", "Write guidance structure in output."},
    {"stopwatch", "Print run time informations."},
    {"min_prob",
     "Minimal probability. Only base pairs of at least this "
     "probability are taken into account."},
    {"max_bps_length_ratio",
     "Maximal ratio of #base pairs divided by sequence length. This serves "
     "as a second filter on the \"significant\" base pairs. [default: 0.0 "
     "= "
     "no effect]."},
    {"max_diff_am", "Maximal difference for sizes of matched arcs. [-1=off]"},
    {"max_diff",
     "Maximal difference for positions of alignment traces (and aligned "
     "bases). "
     "[-1=off]"},
    {"max_diff_at_am",
     "Maximal difference for positions of alignment traces at arc match "
     "ends. "
     "[-1=off]"},
    {"max_diff_alignment_file",
     "Maximal difference relative to given alignment (file in clustalw "
     "format)"},
    {"max_diff_pw_alignment",
     "Maximal difference relative to given alignment (string, "
     "delim=AMPERSAND)"},
    {"max_diff_relax", "Relax deviation constraints in multiple aligmnent"},
    {"min_trace_probability",
     "Minimal sequence alignment probability of potential traces "
     "(probability-based sequence alignment envelope) [default=1e-4]."},
    {"no_lonely_pairs", "Disallow lonely pairs in prediction and alignment."},
    {"max_bp_span", "Limit maximum base pair span [default=off]."},
    {"relaxed_anchors",
     "Use relaxed semantics of anchor constraints [default=strict "
     "semantics]."},
    {"fileA", "Input file 1"}, {"fileB", "Input file 2"},
    {"files",
     "The tool is called with two input files <Input 1> and <Input 2>, "
     "which specify the two input sequences or input "
     "alignments. Different input formats (Fasta, Clustal, Stockholm, "
     "LocARNA PP, ViennaRNA postscript dotplots) are accepted and "
     "automatically recognized (by file content); the two input files can "
     "be "
     "in different formats. Extended variants of the Clustal and Stockholm "
     "formats enable specifying anchor and structure constraints."},

    // mea help
    {"mea_alignment",
     "Perform maximum expected accuracy alignment (instead of using the "
     "default "
     "similarity scoring)."},
    {"match_prob_method",
     "Select method for computing sequence-based base match probablities "
     "(to be used for mea-type alignment scores). Methods: "
     "1=probcons-style "
     "from HMM, 2=probalign-style from PFs, 3=from PFs, local"},
    {"probcons_file",
     "Read parameters for probcons-like calculation of match probabilities "
     "from probcons parameter file."},
    {"temperature_alipf",
     "Temperature for the /sequence alignment/ partition functions used by "
     "the probcons-like sequence-based match/trace probability computation "
     "(this temperature is different from the 'physical' temperature "
     "of RNA folding!)."},
    {"pf_struct_weight",
     "Structure weight in PF computations (for the computation of "
     "sequence-based match probabilties from partition functions)."},
    {"mea_gapcost",
     "Add gap cost contributions (indel and indel-opening) to "
     "the by default gap-cost-free mea score."},
    {"mea_alpha", "Weight alpha for MEA"}, {"mea_beta", "Weight beta for MEA"},
    {"mea_gamma", "Weight gamma for MEA"},
    {"probability_scale", "Scale for probabilities/resolution of mea score"},
    {"write_matchprobs", "Write match probs to file (don't align!)."},
    {"write_traceprobs", "Write trace probs to file (don't align!)."},
    {"read_matchprobs", "Read match probabilities from file."},
    {"write_arcmatch_scores", "Write arcmatch scores (don't align!)"},
    {"read_arcmatch_scores", "Read arcmatch scores."},
    {"read_arcmatch_probs",
     "Read arcmatch probabilities (weighted by factor mea_beta/100)"},

    // locarna-specific help
    {"normalized",
     "Perform normalized local alignment with parameter L. This causes "
     "locarna to compute the best local alignment according to "
     "'Score' / ( L + 'length' ), "
     "where length is the sum of the lengths of the two locally aligned "
     "subsequences. Thus, the larger L, the larger the local alignment; "
     "the size of value L is in the order of local alignment lengths. "
     "Verbose yields info on the iterative optimizations."},
    {"penalized", "Penalized local alignment with penalty PP"},
    {"score_components", "Output components of the score (experimental)."},

    // locarna-P-specific help
    {"min_am_prob",
     "Minimal arc match probability. Write probabilities for only the "
     "arc matchs of at least this probability."},
    {"min_bm_prob",
     "Minimal base match probability. Write probabilities for only the "
     "base matchs of at least this probability."},
    {"pf_scale",
     "Factor for scaling the partition functions. Use in order to avoid "
     "overflow."},
    {"extended_pf",
     "Use extended precision for partition function values. This "
     "increases run-time and space (less than 2x), however enables "
     "handling significantly larger instances."},
    {"extended_pf_sequence_only",
     "Use extended precision for the computation of sequence envelopes. "
     "This "
     "enables "
     "handling significantly larger instances."},
    {"quad_pf",
     "Use quad precision for partition function values. Even more "
     "precision "
     "than "
     "extended pf, but usually much slower (overrides extended-pf)."},
{
    "temperature_alipf",
        "Temperature for the /alignment/ partition functions (this "
        "temperature different from the 'physical' temperature of RNA "
        "folding!). It controls the probability distributions of computed "
        "base and arc match probabilities."
}
