modules/percolator

Rescore peptide-spectrum matches and estimate false discovery rates using the Percolator semi-supervised learning algorithm.

proteomicsspectrum identificationpsmpeptideproteinrescoringfalse discovery ratefeatures

https://github.com/nf-core/modules/[...]/modules/nf-core/percolator

Description

Rescore peptide-spectrum matches and estimate false discovery rates using the Percolator semi-supervised learning algorithm.

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information. e.g. [ id:'sample1' ]

`peptide_identification`
`:file`

peptide identifications as PIN (Percolator input) file

*.pin

Output

name:type

description

pattern

`pout_xml`

`meta`
`:map`

Groovy Map containing sample information. e.g. [ id:'sample1' ]

`${prefix}.pout.xml`
`:file`

Percolator output in XML format containing all PSM-level results

*.pout.xml

`pout_pepxml`

`meta`
`:map`

Groovy Map containing sample information. e.g. [ id:'sample1' ]

`${prefix}.pep.xml`
`:file`

Percolator output in pepXML format

*.pep.xml

`features_pin`

`meta`
`:map`

Groovy Map containing sample information. e.g. [ id:'sample1' ]

`${prefix}.features.pin`
`:file`

Tab-separated file with rescored features (PIN format)

*.features.pin

`weights`

`meta`
`:map`

Groovy Map containing sample information. e.g. [ id:'sample1' ]

`${prefix}.weights.tsv`
`:file`

TSV file containing the final feature weights

*.weights.tsv

`target_peptides`

`meta`
`:map`

Groovy Map containing sample information. e.g. [ id:'sample1' ]

`${prefix}.pep.target.pout`
`:file`

Target peptide-level results in tab separated format (pout)

*.pep.target.pout

`decoy_peptides`

`meta`
`:map`

Groovy Map containing sample information. e.g. [ id:'sample1' ]

`${prefix}.pep.decoy.pout`
`:file`

Decoy peptide-level results in tab separated format (pout)

*.pep.decoy.pout

`target_psms`

`meta`
`:map`

Groovy Map containing sample information. e.g. [ id:'sample1' ]

`${prefix}.psm.target.pout`
`:file`

Target PSM-level results in tab separated format (pout)

*.psm.target.pout

`decoy_psms`

`meta`
`:map`

Groovy Map containing sample information. e.g. [ id:'sample1' ]

`${prefix}.psm.decoy.pout`
`:file`

Decoy PSM-level results in tab separated format (pout)

*.psm.decoy.pout

`target_proteins`

`meta`
`:map`

Groovy Map containing sample information. e.g. [ id:'sample1' ]

`${prefix}.protein.target.pout`
`:file`

Target protein-level results in tab separated format (pout)

*.protein.target.pout

`decoy_proteins`

`meta`
`:map`

Groovy Map containing sample information. e.g. [ id:'sample1' ]

`${prefix}.protein.decoy.pout`
`:file`

Decoy protein-level results in tab separated format (pout)

*.protein.decoy.pout

`versions_percolator`

`${task.process}`
`:string`

The name of the process

`percolator`
`:string`

The name of the tool

`percolator --help 2>&1 | head -1 | sed "s;Percolator version $[^,]$,.;\1;"`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`percolator`
`:string`

The name of the tool

`percolator --help 2>&1 | head -1 | sed "s;Percolator version $[^,]$,.;\1;"`
`:eval`

The expression to obtain the version of the tool

Tools

percolator
Apache-2.0

Semi-supervised learning for peptide identification from shotgun proteomics datasets.

http://percolator.ms https://github.com/percolator/percolator 10.1038/nmeth1113

modules/percolator

Description

Input

meta:map

peptide_identification:file

Output

pout_xml

meta:map

${prefix}.pout.xml:file

pout_pepxml

meta:map

${prefix}.pep.xml:file

features_pin

meta:map

${prefix}.features.pin:file

weights

meta:map

${prefix}.weights.tsv:file

target_peptides

meta:map

${prefix}.pep.target.pout:file

decoy_peptides

meta:map

${prefix}.pep.decoy.pout:file

target_psms

meta:map

${prefix}.psm.target.pout:file

decoy_psms

meta:map

${prefix}.psm.decoy.pout:file

target_proteins

meta:map

${prefix}.protein.target.pout:file

decoy_proteins

meta:map

${prefix}.protein.decoy.pout:file

versions_percolator

${task.process}:string

percolator:string

percolator --help 2>&1 | head -1 | sed "s;Percolator version \([^,]*\),.*;\1;":eval

Topics

versions

${task.process}:string

percolator:string

percolator --help 2>&1 | head -1 | sed "s;Percolator version \([^,]*\),.*;\1;":eval

Tools

percolator Apache-2.0

included in

maintainer

get in touch

`meta`
`:map`

`peptide_identification`
`:file`

`pout_xml`

`meta`
`:map`

`${prefix}.pout.xml`
`:file`

`pout_pepxml`

`meta`
`:map`

`${prefix}.pep.xml`
`:file`

`features_pin`

`meta`
`:map`

`${prefix}.features.pin`
`:file`

`weights`

`meta`
`:map`

`${prefix}.weights.tsv`
`:file`

`target_peptides`

`meta`
`:map`

`${prefix}.pep.target.pout`
`:file`

`decoy_peptides`

`meta`
`:map`

`${prefix}.pep.decoy.pout`
`:file`

`target_psms`

`meta`
`:map`

`${prefix}.psm.target.pout`
`:file`

`decoy_psms`

`meta`
`:map`

`${prefix}.psm.decoy.pout`
`:file`

`target_proteins`

`meta`
`:map`

`${prefix}.protein.target.pout`
`:file`

`decoy_proteins`

`meta`
`:map`

`${prefix}.protein.decoy.pout`
`:file`

`versions_percolator`

`${task.process}`
`:string`

`percolator`
`:string`

`percolator --help 2>&1 | head -1 | sed "s;Percolator version \([^,]\),.;\1;"`
`:eval`

`versions`

`${task.process}`
`:string`

`percolator`
`:string`

`percolator --help 2>&1 | head -1 | sed "s;Percolator version \([^,]\),.;\1;"`
`:eval`

percolator
Apache-2.0