Mercurial > repos > galaxyp > openms_falsediscoveryrate

comparison FalseDiscoveryRate.xml @ 0:7e4bc43844e3 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 12:23:26 -0500
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children 7e170e213707
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-1:000000000000 0:7e4bc43844e3
1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [ID Processing]-->
4 <tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="2.1.0">
5 <description>Estimates the false discovery rate on peptide and protein level using decoy searches.</description>
6 <macros>
7 <token name="@EXECUTABLE@">FalseDiscoveryRate</token>
8 <import>macros.xml</import>
9 </macros>
10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>FalseDiscoveryRate
14
15 #if $param_in:
16 -in $param_in
17 #end if
18 #if $param_in_target:
19 -in_target $param_in_target
20 #end if
21 #if $param_in_decoy:
22 -in_decoy $param_in_decoy
23 #end if
24 #if $param_out:
25 -out $param_out
26 #end if
27 #if $param_proteins_only:
28 -proteins_only
29 #end if
30 #if $param_peptides_only:
31 -peptides_only
32 #end if
33 #if $param_algorithm_no_qvalues:
34 -algorithm:no_qvalues
35 #end if
36 #if $param_algorithm_use_all_hits:
37 -algorithm:use_all_hits
38 #end if
39 #if $param_algorithm_split_charge_variants:
40 -algorithm:split_charge_variants
41 #end if
42 #if $param_algorithm_treat_runs_separately:
43 -algorithm:treat_runs_separately
44 #end if
45 #if $param_algorithm_add_decoy_peptides:
46 -algorithm:add_decoy_peptides
47 #end if
48 #if $adv_opts.adv_opts_selector=='advanced':
49 #if $adv_opts.param_force:
50 -force
51 #end if
52 #end if
53 </command>
54 <inputs>
55 <param name="param_in" type="data" format="idxml" optional="True" label="Identification input file containing a search against a concatenated sequence database" help="(-in) Either specify '-in' alone or 'in_target' together with 'in_decoy' as input"/>
56 <param name="param_in_target" type="data" format="idxml" optional="True" label="Identification input file containing a search against a target-only database" help="(-in_target) "/>
57 <param name="param_in_decoy" type="data" format="idxml" optional="True" label="Identification input file containing a search against a decoy-only database" help="(-in_decoy) "/>
58 <param name="param_proteins_only" display="radio" type="boolean" truevalue="-proteins_only" falsevalue="" checked="false" optional="True" label="If set only the FDR on protein level is calculated" help="(-proteins_only) "/>
59 <param name="param_peptides_only" display="radio" type="boolean" truevalue="-peptides_only" falsevalue="" checked="false" optional="True" label="If set only the FDR on peptide (PSM) level is calculated" help="(-peptides_only) "/>
60 <param name="param_algorithm_no_qvalues" display="radio" type="boolean" truevalue="-algorithm:no_qvalues" falsevalue="" checked="false" optional="True" label="If 'true' strict FDRs will be calculated instead of q-values (the default)" help="(-no_qvalues) "/>
61 <param name="param_algorithm_use_all_hits" display="radio" 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) "/>
62 <param name="param_algorithm_split_charge_variants" display="radio" type="boolean" truevalue="-algorithm:split_charge_variants" falsevalue="" checked="false" optional="True" label="If 'true' charge variants are treated separately (for peptides of combined target/decoy searches only)" help="(-split_charge_variants) "/>
63 <param name="param_algorithm_treat_runs_separately" display="radio" type="boolean" truevalue="-algorithm:treat_runs_separately" falsevalue="" checked="false" optional="True" label="If 'true' different search runs are treated separately (for peptides of combined target/decoy searches only)" help="(-treat_runs_separately) "/>
64 <param name="param_algorithm_add_decoy_peptides" display="radio" type="boolean" truevalue="-algorithm:add_decoy_peptides" falsevalue="" checked="false" optional="True" label="If 'true' decoy peptides will be written to output file, too" help="(-add_decoy_peptides) The q-value is set to the closest target score"/>
65 <expand macro="advanced_options">
66 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
67 </expand>
68 </inputs>
69 <outputs>
70 <data name="param_out" format="idxml"/>
71 </outputs>
72 <help>Estimates the false discovery rate on peptide and protein level using decoy searches.
73
74
75 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FalseDiscoveryRate.html</help>
76 </tool>