Mercurial > repos > galaxyp > openms_falsediscoveryrate

comparison FalseDiscoveryRate.xml @ 3:7e170e213707 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:06:45 -0400
parents 7e4bc43844e3
children f13beb0ac55d
comparison
equal deleted inserted replaced
2:518b1730cf2a 3:7e170e213707
1 <?xml version='1.0' encoding='UTF-8'?> 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.--> 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]--> 3 <!--Proposed Tool Section: [ID Processing]-->
4 <tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="2.1.0"> 4 <tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="2.2.0">
5 <description>Estimates the false discovery rate on peptide and protein level using decoy searches.</description> 5 <description>Estimates the false discovery rate on peptide and protein level using decoy searches.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FalseDiscoveryRate</token> 7 <token name="@EXECUTABLE@">FalseDiscoveryRate</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
13 <command>FalseDiscoveryRate 13 <command>FalseDiscoveryRate
14 14
15 #if $param_in: 15 #if $param_in:
16 -in $param_in 16 -in $param_in
17 #end if 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: 18 #if $param_out:
25 -out $param_out 19 -out $param_out
26 #end if 20 #end if
27 #if $param_proteins_only: 21 #if $param_PSM:
28 -proteins_only 22 -PSM
23 #if " " in str($param_PSM):
24 "$param_PSM"
25 #else
26 $param_PSM
27 #end if
29 #end if 28 #end if
30 #if $param_peptides_only: 29 #if $param_protein:
31 -peptides_only 30 -protein
31 #if " " in str($param_protein):
32 "$param_protein"
33 #else
34 $param_protein
35 #end if
36 #end if
37 #if $param_FDR_PSM:
38 -FDR:PSM $param_FDR_PSM
39 #end if
40 #if $param_FDR_protein:
41 -FDR:protein $param_FDR_protein
32 #end if 42 #end if
33 #if $param_algorithm_no_qvalues: 43 #if $param_algorithm_no_qvalues:
34 -algorithm:no_qvalues 44 -algorithm:no_qvalues
35 #end if 45 #end if
36 #if $param_algorithm_use_all_hits: 46 #if $param_algorithm_use_all_hits:
50 -force 60 -force
51 #end if 61 #end if
52 #end if 62 #end if
53 </command> 63 </command>
54 <inputs> 64 <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"/> 65 <param name="param_in" type="data" format="idxml" optional="False" label="Identifications from searching a target-decoy database" help="(-in) "/>
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) "/> 66 <param name="param_PSM" display="radio" type="select" optional="False" value="true" label="Perform FDR calculation on PSM level" help="(-PSM) ">
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) "/> 67 <option value="true" selected="true">true</option>
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) "/> 68 <option value="false">false</option>
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) "/> 69 </param>
70 <param name="param_protein" display="radio" type="select" optional="False" value="true" label="Perform FDR calculation on protein level" help="(-protein) ">
71 <option value="true" selected="true">true</option>
72 <option value="false">false</option>
73 </param>
74 <param name="param_FDR_PSM" type="float" min="0.0" max="1.0" optional="True" value="1.0" label="Filter PSMs based on q-value (" help="(-PSM) e.g., 0.05 = 5% FDR, disabled for 1)"/>
75 <param name="param_FDR_protein" type="float" min="0.0" max="1.0" optional="True" value="1.0" label="Filter proteins based on q-value (" help="(-protein) e.g., 0.05 = 5% FDR, disabled for 1)"/>
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) "/> 76 <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) "/> 77 <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) "/> 78 <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) "/> 79 <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"/> 80 <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"/>