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PangenomeOrthomcl.spec
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PangenomeOrthomcl.spec
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/*
A KBase module: PangenomeOrthomcl
*/
module PangenomeOrthomcl {
/*
Indicates true or false values, false = 0, true = 1
@range [0,1]
*/
typedef int boolean;
/*
Name of workspace.
*/
typedef string workspace;
/*
The workspace ID for a GenomeSet data object.
@id ws KBaseGenome.Genome
*/
typedef string ws_genome_id;
/*
The workspace ID for a GenomeSet data object.
@id ws KBaseSearch.GenomeSet
*/
typedef string ws_genomeset_id;
/*
The workspace ID for a Pangenome data object.
@id ws KBaseGenomes.Pangenome
*/
typedef string ws_pangenome_id;
/*
Input parameters of build_pangenome_with_orthomcl method.
input_genomeset_ref - optional input reference to genome set
object (alternative way is input_genome_refs);
input_genome_refs - optional input list of references to
genome objects (alternative way is input_genomeset_ref);
output_workspace - workspace for saving resulting pangenome;
output_pangenome_id - name of resulting pangenome object;
num_descriptions - [blastp, -v] Store one-line descriptions for
this number of database sequences. Default value is 100000.
num_alignments - [blastp, -b] Store alignments for this number of
database sequences. Default value is 100000.
evalue - [blastp, -e] Expect value (E) for saving hits. Default
value is 1e-5.
word_size - [blastp, -W] Word size of initial match. Valid word
sizes are 2-7. Default value is 3.
gapopen - [blastp, -G] Cost to open a gap. Default value is 11.
gapextend - [blastp, -E] Cost to extend a gap. Default value is 1.
matrix - [blastp, -M] Scoring matrix name. Default value is BLOSUM62.
threshold - [blastp, -f] Minimum score to add a word to the BLAST
lookup table. Default value is 11.
comp_based_stats - [blastp, -C] Use composition-based statistics
(0: no composition-based statistics; 1: Composition-based
statistics as in NAR 29:2994-3005, 2001; 2: Composition-based
score adjustments as in Bioinformatics 21:902-911, 2005,
conditioned on sequence properties; 3 - Composition-based
score adjustment as in Bioinformatics 21:902-911, 2005,
unconditionally). Default value is 2.
seg - [blastp, -F] Filter query sequence with SEG (yes/no). Default
value is yes.
lcase_masking - [blastp, -U] Use lower case filtering in query and
subject sequence(s). Default value is false(0).
xdrop_gap_final - [blastp, -Z] Heuristic value (in bits) for final
gapped alignment. Default value is 25.
window_size - [blastp, -A] Multiple hits window size, use 0 to
specify 1-hit algorithm. Default value is 40.
use_sw_tback - [blastp, -s] Compute locally optimal Smith-Waterman
alignments. Default value is false(0).
mcl_p - [mcl, -P] Prune number. Default value is 10000.
mcl_s - [mcl, -S] Selection number. Default value is 1100.
mcl_r - [mcl, -R] Recovery number. Default value is 1400.
mcl_pct - [mcl, -pct] Recovery percentage. Default value is 90.
mcl_warn_p - [mcl, -warn-p] Warn if pruning reduces mass to this
weight. Default value is 10.
mcl_warn_factor - [mcl, -warn-factor] Warn if pruning reduces entry
count by this value. Default value is 1000.
mcl_init_l - [mcl, -l] Initial loop length. Default value is 0.
mcl_main_l - [mcl, -L] Main loop length. Default value is 10000.
mcl_init_i - [mcl, -i] Initial inflation. Default value is 2.0.
mcl_main_i - [mcl, -I] Main inflation. Default value is 1.5.
*/
typedef structure {
ws_genomeset_id input_genomeset_ref;
list<ws_genome_id> input_genome_refs;
workspace output_workspace;
ws_pangenome_id output_pangenome_id;
int num_descriptions;
int num_alignments;
string evalue;
int word_size;
int gapopen;
int gapextend;
string matrix;
int threshold;
string comp_based_stats;
string seg;
boolean lcase_masking;
float xdrop_gap_final;
int window_size;
boolean use_sw_tback;
int mcl_p;
int mcl_s;
int mcl_r;
int mcl_pct;
int mcl_warn_p;
int mcl_warn_factor;
int mcl_init_l;
int mcl_main_l;
float mcl_init_i;
float mcl_main_i;
} BuildPangenomeWithOrthmclParams;
/*
Output results of build_pangenome_with_orthomcl method.
One of 'pangenome_ref' and 'error' fields should be defined.
*/
typedef structure {
ws_pangenome_id pangenome_ref;
string report_name;
string report_ref;
} BuildPangenomeWithOrthmclResult;
funcdef build_pangenome_with_orthomcl(BuildPangenomeWithOrthmclParams params)
returns (BuildPangenomeWithOrthmclResult) authentication required;
};