|
0
|
1 <?xml version='1.0' encoding='UTF-8'?>
|
|
|
2 <tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="1.12.0">
|
|
|
3 <description>Estimates the false discovery rate on peptide and protein level using decoy searches.</description>
|
|
|
4 <macros>
|
|
|
5 <token name="@EXECUTABLE@">FalseDiscoveryRate</token>
|
|
|
6 <import>macros.xml</import>
|
|
|
7 </macros>
|
|
|
8 <expand macro="stdio"/>
|
|
|
9 <expand macro="requirements"/>
|
|
|
10 <command>FalseDiscoveryRate
|
|
|
11
|
|
|
12 -in ${param_in}
|
|
|
13 -fwd_in ${param_fwd_in}
|
|
|
14 -rev_in ${param_rev_in}
|
|
|
15 -out ${param_out}
|
|
|
16 ${param_proteins_only}
|
|
|
17 ${param_peptides_only}
|
|
|
18 -threads \${GALAXY_SLOTS:-24}
|
|
|
19 ${param_q_value}
|
|
|
20 ${param_use_all_hits}
|
|
|
21 ${param_split_charge_variants}
|
|
|
22 ${param_treat_runs_separately}
|
|
|
23 -algorithm:decoy_string ${param_decoy_string}
|
|
|
24 ${param_add_decoy_peptides}
|
|
|
25 </command>
|
|
|
26 <inputs>
|
|
|
27 <param name="param_in" type="data" format="idXML" optional="True" label="Identification input file which contains a search against a concatenated sequence database. Either specify '-in' alone or 'fwd_in' together with 'rev_in' as input." help="(-in)"/>
|
|
|
28 <param name="param_fwd_in" type="data" format="idXML" optional="True" label="Identification input to estimate FDR, forward run." help="(-fwd_in)"/>
|
|
|
29 <param name="param_rev_in" type="data" format="idXML" optional="True" label="Identification input to estimate FDR, decoy run." help="(-rev_in)"/>
|
|
|
30 <param name="param_proteins_only" type="boolean" truevalue="-proteins_only true" falsevalue="-proteins_only false" checked="false" optional="True" label="If set, the FDR of the proteins only is calculated" help="(-proteins_only)"/>
|
|
|
31 <param name="param_peptides_only" type="boolean" truevalue="-peptides_only true" falsevalue="-peptides_only false" checked="false" optional="True" label="If set, the FDR of the peptides only is calculated" help="(-peptides_only)"/>
|
|
|
32 <param name="param_q_value" type="boolean" truevalue="-algorithm:q_value true" falsevalue="-algorithm:q_value false" checked="true" optional="True" label="If 'true', the q-values will be calculated instead of the FDRs" help="(-q_value)"/>
|
|
|
33 <param name="param_use_all_hits" type="boolean" truevalue="-algorithm:use_all_hits true" falsevalue="-algorithm:use_all_hits false" checked="false" optional="True" label="If 'true' not only the first hit, but all are used (peptides only)" help="(-use_all_hits)"/>
|
|
|
34 <param name="param_split_charge_variants" type="boolean" truevalue="-algorithm:split_charge_variants true" falsevalue="-algorithm:split_charge_variants false" checked="false" optional="True" label="If set to 'true' charge variants are treated separately (for peptides of combined target/decoy searches only)." help="(-split_charge_variants)"/>
|
|
|
35 <param name="param_treat_runs_separately" type="boolean" truevalue="-algorithm:treat_runs_separately true" falsevalue="-algorithm:treat_runs_separately false" checked="false" optional="True" label="If set to 'true' different search runs are treated separately (for peptides of combined target/decoy searches only)." help="(-treat_runs_separately)"/>
|
|
|
36 <param name="param_decoy_string" type="text" size="20" value="_rev" label="String which is appended at the accession of the protein to indicate that it is a decoy protein (for proteins only)." help="(-decoy_string)"/>
|
|
|
37 <param name="param_add_decoy_peptides" type="boolean" truevalue="-algorithm:add_decoy_peptides true" falsevalue="-algorithm:add_decoy_peptides false" checked="false" optional="True" label="If set to true, decoy peptides will be written to output file, too. The q-value is set to the closest target score." help="(-add_decoy_peptides)"/>
|
|
|
38 </inputs>
|
|
|
39 <outputs>
|
|
|
40 <data name="param_out" label="Identification output with annotated FDR" format="idXML"/>
|
|
|
41 </outputs>
|
|
|
42 <help>**What it does**
|
|
|
43
|
|
|
44 Estimates the false discovery rate on peptide and protein level using decoy searches.
|
|
|
45
|
|
|
46
|
|
|
47 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FalseDiscoveryRate.html
|
|
|
48
|
|
|
49 @REFERENCES@
|
|
|
50 </help>
|
|
|
51 </tool>
|
