class DadaSEForm(JobDetailsForm):
"""
Defines the form for the DADA2 single-end pipeline.
"""
ion_torrent = BooleanField("Check if Ion Torrent sequence",
default=False,
description=dada_help.ion_torrent_seq)
zero_or_g = 'Must be 0 or greater.'
trimleft_fwd = IntegerField("Trim left",
default=20,
description=dada_help.trim_left_fwd_desc,
validators=[
neph_validators.greater_than(
message=zero_or_g, minimum=-1)
])
truncQ = IntegerField("Truncation quality score",
default=4,
description=dada_help.tuncq_desc,
validators=[
neph_validators.greater_than(
message="Must be greater than 0.",
minimum=-1)
])
truncLen_fwd = IntegerField("Truncation length",
default=0,
description=dada_help.truncLen_fwd_desc,
validators=[
neph_validators.greater_than(
message="Must be greater than 0.",
minimum=-1)
])
maxEE = IntegerField("Maximum expected errors",
default=5,
description=dada_help.maxee_desc,
validators=[
neph_validators.greater_than(
message="Must be greater than 0.", minimum=-1)
])
chimera = BooleanField("Run chimera removal",
default=True,
description=dada_help.remove_chimera_desc)
taxmethod = SelectField("Taxonomic assigment",
default="rdp",
description=dada_help.tax_method,
choices=[("rdp", "rdp"), ("idtaxa", "IDTAXA")])
sampling_depth = IntegerField(
"Sampling depth for downstream analysis",
description=dada_help.sampling_depth_desc,
validators=[
Optional(),
neph_validators.greater_than(
message="Must be greater than or equal to 0.", minimum=0)
])
ref_db = SelectField("Reference Database",
default="SILVA v132",
description=dada_help.ref_db_desc,
choices=[("sv99", "SILVA v132"),
("gg97", "Greengenes v13.8"),
("homd", "HOMD")])
class DSAnalysisForm(JobDetailsForm):
gt_five = "Input is required, must an integer greater than 5."
desc = "The total frequency that each sample should be rarefied to prior "\
"to computing diversity metrics. Samples with counts below this "\
"value will be removed from the analysis."
sampling_depth = IntegerField("Sampling depth for downstream analysis",
description=desc,
validators=[
InputRequired(),
neph_validators.greater_than(
message=gt_five, minimum=4)
])
red_warn = '<span style="color: red;">Requires Treatment Group column in \
mapping file, after filtering by sampling depth, to contain at least \
2 groups, and each group to contain at least 2 samples.</span>'
link = '<a class="" href="da_details/#input-files-and-parameters" \
target="_blank" rel="noopener noreferrer">More information.</a>'
alpha_desc = "Run alpha diversity statistical comparisons between groups, \
and produce alpha diversity plots. {} {}".format(red_warn, link)
alpha_group_sig = BooleanField("Run Alpha group significance",
default=False,
description=alpha_desc)
class QiimeBaseOptions(JobDetailsForm):
"""
Defines the options that are common to (almost) all QIIME pipes.
"""
phred_quality = IntegerField(
"Minimum phred quality score",
default=19,
description=qiime_help.qiime_base_phred_qual_desc)
phred_offset = IntegerField(
"Phred offset",
default=33,
description=qiime_help.qiime_base_phred_offset_desc)
max_n = IntegerField("Maximum ambiguous",
default=0,
description=qiime_help.qiime_pe_max_ambiguous_desc)
max_bad_run = IntegerField(
"Max bad run length",
default=3,
description=qiime_help.qiime_max_bad_run_length_desc)
ref_db = SelectField("OTU Picking Database",
default="sv99",
description=qiime_help.qiime_base_database_desc,
choices=[("sv99", "SILVA 99 v132"),
("sv97", "SILVA 97 v132"),
("gg99", "Greengenes 99 v13.5"),
("gg97", "Greengenes 97 v13.5"),
("homd", "HOMD")])
picrust = BooleanField("Run PICRUSt annotations",
default=False,
description=qiime_help.qiime_picrust_desc)
otu_strategy = SelectField(
"Analysis type",
default="OPEN_REFERENCE",
description=qiime_help.qiime_base_analysis_type_desc,
choices=[("open", "Open Reference"), ("closed", "Closed Reference"),
("de_novo", "De Novo")])
sampling_depth = IntegerField(
"Sampling depth for downstream analysis",
description=qiime_help.sampling_depth_desc,
validators=[
Optional(),
greater_than(message="Must be greater than or equal to 0.",
minimum=0)
])
class QiimePEITSForm(JobDetailsForm):
"""
Defines the form for the QIIME ITS PE pipe.
"""
phred_quality = IntegerField(
"Minimum phred quality score",
default=19,
description=qiime_help.qiime_base_phred_qual_desc)
phred_offset = IntegerField(
"Phred offset",
default=33,
description=qiime_help.qiime_base_phred_offset_desc)
max_n = IntegerField("Maximum ambiguous",
default=0,
description=qiime_help.qiime_pe_max_ambiguous_desc)
max_bad_run = IntegerField(
"Maximum bad run length",
default=3,
description=qiime_help.qiime_its_max_bad_run_length_desc)
min_overlap = IntegerField("Minimum overlap length",
default=10,
description=qiime_help.qiime_min_overlap_desc)
perc_max_diff = IntegerField(
"Percent difference within overlap",
default=25,
description=qiime_help.qiime_percent_max_diff_desc)
ref_db = SelectField("Reference Database",
default="ITS_99",
description=qiime_help.qiime_its_ref_db_desc,
choices=[("its99", "ITS 99"), ("its97", "ITS 97")])
sampling_depth = IntegerField(
"Sampling depth for downstream analysis",
description=qiime_help.sampling_depth_desc,
validators=[
Optional(),
greater_than(message="Must be greater than or equal to 0.",
minimum=0)
])
otu_strategy = SelectField(
"Analysis type",
default="OPEN_REFERENCE",
description=qiime_help.qiime_base_analysis_type_desc,
choices=[("open", "Open Reference"), ("closed", "Closed Reference"),
("de_novo", "De Novo")])
class MothurPEForm(JobDetailsForm):
"""
Defines the pipeline options form for Mothur FASTQ Paired-End.
"""
maxlength = IntegerField(
"Max length *",
default=0,
description=mothur_help.mothur_max_seq_length_desc)
remove_lineage = MultiDashedCheckboxField(
"Remove sequences that belong to taxa of certain lineages",
default=["Chloroplast", "Mitochondria", "unknown", "Eukaryote"],
description=mothur_help.mothur_remove_lineage_desc,
choices=[("Archaea", "Archaea"), ("unknown", "unknown"),
("Chloroplast", "Chloroplast"),
("Mitochondria", "Mitochondria"), ("Eukaryote", "Eukaryote")])
optimize = SelectField(
"Optimize",
default="start-end",
description=mothur_help.mothur_optimize_criteria_desc,
choices=[("start-end", "start-end"), ("start", "start"),
("end", "end")])
criteria = IntegerField(
"Criteria",
default=90,
description=mothur_help.mothur_optimize_criteria_desc)
ref_db = SelectField("OTU Picking Reference Database",
default="SILVA",
description=mothur_help.mothur_reference_db_desc,
choices=[("sv99", "SILVA 99"), ("homd", "HOMD")])
picrust = BooleanField("Run PICRUSt annotations",
default=False,
description=mothur_help.mothur_picrust_desc)
sampling_depth = IntegerField(
"Sampling depth for downstream analysis",
description=mothur_help.sampling_depth_desc,
validators=[
Optional(),
greater_than(message="Must be greater than or equal to 0.",
minimum=0)
])