Docstring:
Usage: qiime autopepsirf diffEnrich-deconv-tsv [OPTIONS]
Uses the diff normalization from pepsirf to generate z scores that are used
to determine enriched peptides and **ADD DECONV DESCRIPTION**
Parameters:
--p-raw-data-tsv TEXT [required]
--p-bins-tsv TEXT [required]
--p-linked-tsv TEXT [required]
--p-deconv-threshold INTEGER
[required]
--p-mapfile-suffix TEXT [required]
--p-outfile-suffix TEXT [required]
--p-id-name-map-tsv TEXT
[optional]
--p-infer-pairs-source / --p-no-infer-pairs-source
Infer sample pairs from names. This option assumes
names of replicates will be identical with the
exception of a final string denoted with a '_'. For
example, these names would be considered two
replicates of the same sample: VW_100_1X_A and
VW_100_1X_B [default: True]
--p-flexible-reps-source / --p-no-flexible-reps-source
Will infer the number of replicates for each sample
based on sample names, and will not require any
specific number of replicates for inclusion.
Therefore, some samples may have a single replicate,
some may have 2, 3, 4 etc. And all replicates of a
given sample will be considered for determining
enriched peptides. [default: False]
--p-s-enrich-source / --p-no-s-enrich-source
All samples will be processed individually as
samples with only one replicate [default: False]
--m-user-defined-source-file METADATA
--m-user-defined-source-column COLUMN MetadataColumn[Categorical]
Metadata file containing all sample names and their
source groups. Used to create pairs tsv to run
pepsirf enrich module. [optional]
--p-negative-control-tsv TEXT
[optional]
--p-negative-id TEXT Optional approach for identifying negative
controls. Provide a unique string at the start of
all negative control samples. [optional]
--p-negative-names TEXT...
List[Str] Optional approach for identifying negative
controls. Space-separated list of negative control
sample names. [optional]
--p-thresh-file-tsv TEXT
[optional]
--p-exact-z-thresh TEXT Individual Exact z score threshold separated by a
comma for creation of threshold file to run
pepsirf's enrich module (Ex: 6,10 or 30) [optional]
--p-exact-cs-thresh TEXT
Individual Exact col-sum threshold separated by a
comma for creation of threshold file to run
pepsirf's enrich module (Ex: 6,10 or 30)
[default: '20']
--p-exact-zenrich-thresh TEXT...
List[Str] List of exact z score thresholds either individual
or combined. List MUST BE in descending order.
(Example argument: '--p-exact-zenrich-thresh 25 10
3' or '--p-exact-zenrich-thresh 6,25 4,10 1,3')
[optional]
--p-pepsirf-tsv-dir TEXT
Provide a directory path. Must also provide
tsv-base-str for output of tsv verison of qza files.
The source_samples file and png boxplot outputs will
always be put within this directory. [default: './']
--p-tsv-base-str TEXT The base name for the output tsv files excluding ay
extensions, typcally the raw data filename (EX:
--p-tsv-base-str raw_data). Must also provide
pepsirf-tsv-dir, if pepsirf-tsv-dir provided without
tsv-base-str, the default will be 'aps-output'.
[optional]
--p-step-z-thresh INTEGER
Range(1, None) Integar to increment z-score thresholds.
[default: 5]
--p-upper-z-thresh INTEGER
Range(2, None) Upper limit of z-score thresholds (non-inclusive).
[default: 30]
--p-lower-z-thresh INTEGER
Range(1, None) Lower limit of z-score thresholds (inclusive).
[default: 5]
--p-raw-constraint INTEGER
Range(0, None) The minimum total raw count across all peptides for
a sample to be included in the analysis. This
provides a way to impose a minimum read count for a
sample to be evaluated. [default: 300000]
--p-hdi PROPORTION Alternative approach for discarding outliers prior
Range(0.0, 1.0) to calculating mean and stdev. If provided, this
argument will override --trim, which trims evenly
from both sides of the distribution. For --hdi, the
user should provide the high density interval to be
used for calculation of mean and stdev. For example,
'--hdi 0.95' would instruct the program to utilize
the 95% highest density interval (from each bin) for
these calculations. [default: 0.95]
--p-scoring-strategy TEXT
[default: 'summation']
--p-score-filtering / --p-no-score-filtering
[default: False]
--p-score-tie-threshold NUMBER
[default: 0.0]
--p-score-overlap-threshold NUMBER
[default: 0.0]
--p-single-threaded / --p-no-single-threaded
[default: False]
--p-remove-file-types / --p-no-remove-file-types
[default: False]
--p-pepsirf-binary TEXT The binary to call pepsirf on your system.
[default: 'pepsirf']
Outputs:
--o-dir-out ARTIFACT
DeconvBatch [required]
--o-score-per-round ARTIFACT
ScorePerRound [required]
--o-map-dir ARTIFACT
PeptideAssignmentMap [required]
--o-col-sum ARTIFACT
FeatureTable[Normed] [required]
--o-diff ARTIFACT FeatureTable[NormedDifference]
[required]
--o-diff-ratio ARTIFACT FeatureTable[NormedDiffRatio]
[required]
--o-zscore ARTIFACT
FeatureTable[Zscore] [required]
--o-zscore-nan ARTIFACT
ZscoreNan [required]
--o-sample-names ARTIFACT
InfoSNPN [required]
--o-read-counts ARTIFACT
InfoSumOfProbes [required]
--o-rc-boxplot VISUALIZATION
[required]
--o-enrich ARTIFACT
PairwiseEnrichment [required]
--o-enrich-count-boxplot VISUALIZATION
[required]
--o-zscore-scatter VISUALIZATION
[required]
--o-colsum-scatter VISUALIZATION
[required]
--o-zenrich-scatter VISUALIZATION
[required]
Miscellaneous:
--output-dir PATH Output unspecified results to a directory
--verbose / --quiet Display verbose output to stdout and/or stderr
during execution of this action. Or silence output
if execution is successful (silence is golden).
--recycle-pool TEXT Use a cache pool for pipeline resumption. QIIME 2
will cache your results in this pool for reuse by
future invocations. These pool are retained until
deleted by the user. If not provided, QIIME 2 will
create a pool which is automatically reused by
invocations of the same action and removed if the
action is successful. Note: these pools are local to
the cache you are using.
--no-recycle Do not recycle results from a previous failed
pipeline run or save the results from this run for
future recycling.
--parallel Execute your action in parallel. This flag will use
your default parallel config.
--parallel-config FILE Execute your action in parallel using a config at
the indicated path.
--use-cache DIRECTORY Specify the cache to be used for the intermediate
work of this pipeline. If not provided, the default
cache under $TMP/qiime2/ will be used.
IMPORTANT FOR HPC USERS: If you are on an HPC system
and are using parallel execution it is important to
set this to a location that is globally accessible
to all nodes in the cluster.
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Import:
from qiime2.plugins.autopepsirf.pipelines import diffEnrich_deconv_tsv
Docstring:
diffEnrich deconv Pepsirf Pipeline
Uses the diff normalization from pepsirf to generate z scores that are used
to determine enriched peptides and **ADD DECONV DESCRIPTION**
Parameters
----------
raw_data_tsv : Str
bins_tsv : Str
linked_tsv : Str
deconv_threshold : Int
mapfile_suffix : Str
outfile_suffix : Str
id_name_map_tsv : Str, optional
infer_pairs_source : Bool, optional
Infer sample pairs from names. This option assumes names of replicates
will be identical with the exception of a final string denoted with a
'_'. For example, these names would be considered two replicates of the
same sample: VW_100_1X_A and VW_100_1X_B
flexible_reps_source : Bool, optional
Will infer the number of replicates for each sample based on sample
names, and will not require any specific number of replicates for
inclusion. Therefore, some samples may have a single replicate, some
may have 2, 3, 4 etc. And all replicates of a given sample will be
considered for determining enriched peptides.
s_enrich_source : Bool, optional
All samples will be processed individually as samples with only one
replicate
user_defined_source : MetadataColumn[Categorical], optional
Metadata file containing all sample names and their source groups. Used
to create pairs tsv to run pepsirf enrich module.
negative_control_tsv : Str, optional
negative_id : Str, optional
Optional approach for identifying negative controls. Provide a unique
string at the start of all negative control samples.
negative_names : List[Str], optional
Optional approach for identifying negative controls. Space-separated
list of negative control sample names.
thresh_file_tsv : Str, optional
exact_z_thresh : Str, optional
Individual Exact z score threshold separated by a comma for creation of
threshold file to run pepsirf's enrich module (Ex: 6,10 or 30)
exact_cs_thresh : Str, optional
Individual Exact col-sum threshold separated by a comma for creation of
threshold file to run pepsirf's enrich module (Ex: 6,10 or 30)
exact_zenrich_thresh : List[Str], optional
List of exact z score thresholds either individual or combined. List
MUST BE in descending order. (Example argument: '--p-exact-zenrich-
thresh 25 10 3' or '--p-exact-zenrich-thresh 6,25 4,10 1,3')
pepsirf_tsv_dir : Str, optional
Provide a directory path. Must also provide tsv-base-str for output of
tsv verison of qza files. The source_samples file and png boxplot
outputs will always be put within this directory.
tsv_base_str : Str, optional
The base name for the output tsv files excluding ay extensions,
typcally the raw data filename (EX: --p-tsv-base-str raw_data). Must
also provide pepsirf-tsv-dir, if pepsirf-tsv-dir provided without tsv-
base-str, the default will be 'aps-output'.
step_z_thresh : Int % Range(1, None), optional
Integar to increment z-score thresholds.
upper_z_thresh : Int % Range(2, None), optional
Upper limit of z-score thresholds (non-inclusive).
lower_z_thresh : Int % Range(1, None), optional
Lower limit of z-score thresholds (inclusive).
raw_constraint : Int % Range(0, None), optional
The minimum total raw count across all peptides for a sample to be
included in the analysis. This provides a way to impose a minimum read
count for a sample to be evaluated.
hdi : Float % Range(0.0, 1.0), optional
Alternative approach for discarding outliers prior to calculating mean
and stdev. If provided, this argument will override --trim, which trims
evenly from both sides of the distribution. For --hdi, the user should
provide the high density interval to be used for calculation of mean
and stdev. For example, '--hdi 0.95' would instruct the program to
utilize the 95% highest density interval (from each bin) for these
calculations.
scoring_strategy : Str, optional
score_filtering : Bool, optional
score_tie_threshold : Float, optional
score_overlap_threshold : Float, optional
single_threaded : Bool, optional
remove_file_types : Bool, optional
pepsirf_binary : Str, optional
The binary to call pepsirf on your system.
Returns
-------
dir_out : DeconvBatch
score_per_round : ScorePerRound
map_dir : PeptideAssignmentMap
col_sum : FeatureTable[Normed]
diff : FeatureTable[NormedDifference]
diff_ratio : FeatureTable[NormedDiffRatio]
zscore : FeatureTable[Zscore]
zscore_nan : ZscoreNan
sample_names : InfoSNPN
read_counts : InfoSumOfProbes
rc_boxplot : Visualization
enrich : PairwiseEnrichment
enrich_count_boxplot : Visualization
zscore_scatter : Visualization
colsum_scatter : Visualization
zenrich_scatter : Visualization
