0
|
1 <?xml version='1.0' encoding='UTF-8'?>
|
|
2 <tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="2.0.0">
|
|
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 #if $param_in:
|
|
13 -in $param_in
|
|
14 #end if
|
|
15 #if $param_fwd_in:
|
|
16 -fwd_in $param_fwd_in
|
|
17 #end if
|
|
18 #if $param_rev_in:
|
|
19 -rev_in $param_rev_in
|
|
20 #end if
|
|
21 #if $param_out:
|
|
22 -out $param_out
|
|
23 #end if
|
|
24 #if $param_proteins_only:
|
|
25 -proteins_only
|
|
26 #end if
|
|
27 #if $param_peptides_only:
|
|
28 -peptides_only
|
|
29 #end if
|
|
30 -threads \${GALAXY_SLOTS:-24}
|
|
31 #if $param_algorithm_q_value:
|
|
32 -algorithm:q_value
|
|
33 #end if
|
|
34 #if $param_algorithm_use_all_hits:
|
|
35 -algorithm:use_all_hits
|
|
36 #end if
|
|
37 #if $param_algorithm_split_charge_variants:
|
|
38 -algorithm:split_charge_variants
|
|
39 #end if
|
|
40 #if $param_algorithm_treat_runs_separately:
|
|
41 -algorithm:treat_runs_separately
|
|
42 #end if
|
|
43 #if $param_algorithm_decoy_string:
|
|
44 -algorithm:decoy_string "$param_algorithm_decoy_string"
|
|
45 #end if
|
|
46 #if $param_algorithm_add_decoy_peptides:
|
|
47 -algorithm:add_decoy_peptides
|
|
48 #end if
|
|
49 #if $adv_opts.adv_opts_selector=='advanced':
|
|
50 #if $adv_opts.param_force:
|
|
51 -force
|
|
52 #end if
|
|
53 #end if
|
|
54 </command>
|
|
55 <inputs>
|
|
56 <param name="param_in" type="data" format="idxml" optional="True" label="Identification input file which contains a search against a concatenated sequence database" help="(-in) Either specify '-in' alone or 'fwd_in' together with 'rev_in' as input"/>
|
|
57 <param name="param_fwd_in" type="data" format="idxml" optional="True" label="Identification input to estimate FDR, forward run" help="(-fwd_in) "/>
|
|
58 <param name="param_rev_in" type="data" format="idxml" optional="True" label="Identification input to estimate FDR, decoy run" help="(-rev_in) "/>
|
|
59 <param name="param_proteins_only" type="boolean" truevalue="-proteins_only" falsevalue="" checked="false" optional="True" label="If set, the FDR of the proteins only is calculated" help="(-proteins_only) "/>
|
|
60 <param name="param_peptides_only" type="boolean" truevalue="-peptides_only" falsevalue="" checked="false" optional="True" label="If set, the FDR of the peptides only is calculated" help="(-peptides_only) "/>
|
|
61 <param name="param_algorithm_q_value" type="boolean" truevalue="-algorithm:q_value" falsevalue="" checked="true" optional="True" label="If 'true', the q-values will be calculated instead of the FDRs" help="(-q_value) "/>
|
|
62 <param name="param_algorithm_use_all_hits" type="boolean" truevalue="-algorithm:use_all_hits" falsevalue="" checked="false" optional="True" label="If 'true' not only the first hit, but all are used (peptides only)" help="(-use_all_hits) "/>
|
|
63 <param name="param_algorithm_split_charge_variants" type="boolean" truevalue="-algorithm:split_charge_variants" falsevalue="" 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) "/>
|
|
64 <param name="param_algorithm_treat_runs_separately" type="boolean" truevalue="-algorithm:treat_runs_separately" falsevalue="" 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) "/>
|
|
65 <param name="param_algorithm_decoy_string" type="text" size="30" 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) ">
|
|
66 <sanitizer>
|
|
67 <valid initial="string.printable">
|
|
68 <remove value="'"/>
|
|
69 <remove value="""/>
|
|
70 </valid>
|
|
71 </sanitizer>
|
|
72 </param>
|
|
73 <param name="param_algorithm_add_decoy_peptides" type="boolean" truevalue="-algorithm:add_decoy_peptides" falsevalue="" checked="false" optional="True" label="If set to true, decoy peptides will be written to output file, too" help="(-add_decoy_peptides) The q-value is set to the closest target score"/>
|
|
74 <expand macro="advanced_options">
|
|
75 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
|
|
76 </expand>
|
|
77 </inputs>
|
|
78 <outputs>
|
|
79 <data name="param_out" format="idxml"/>
|
|
80 </outputs>
|
|
81 <help>**What it does**
|
|
82
|
|
83 Estimates the false discovery rate on peptide and protein level using decoy searches.
|
|
84
|
|
85
|
|
86 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FalseDiscoveryRate.html</help>
|
|
87 <expand macro="references"/>
|
|
88 </tool>
|