Mercurial > repos > galaxyp > openms_falsediscoveryrate

annotate FalseDiscoveryRate.xml @ 7:f13beb0ac55d draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author galaxyp
date Mon, 12 Feb 2018 13:01:39 -0500
parents 7e170e213707
children 7cc2a2687bff
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [ID Processing]-->
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4 <tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="2.3.0">
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5 <description>Estimates the false discovery rate on peptide and protein level using decoy searches.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FalseDiscoveryRate</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>FalseDiscoveryRate
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 #if $param_PSM:
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22 -PSM
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23 #if " " in str($param_PSM):
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24 "$param_PSM"
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25 #else
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26 $param_PSM
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27 #end if
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28 #end if
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29 #if $param_protein:
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30 -protein
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31 #if " " in str($param_protein):
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32 "$param_protein"
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33 #else
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34 $param_protein
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35 #end if
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36 #end if
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37 #if $param_FDR_PSM:
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38 -FDR:PSM $param_FDR_PSM
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39 #end if
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40 #if $param_FDR_protein:
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41 -FDR:protein $param_FDR_protein
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42 #end if
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43 #if $param_algorithm_no_qvalues:
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44 -algorithm:no_qvalues
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45 #end if
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46 #if $param_algorithm_use_all_hits:
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47 -algorithm:use_all_hits
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48 #end if
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49 #if $param_algorithm_split_charge_variants:
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50 -algorithm:split_charge_variants
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51 #end if
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52 #if $param_algorithm_treat_runs_separately:
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53 -algorithm:treat_runs_separately
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54 #end if
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55 #if $param_algorithm_add_decoy_peptides:
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56 -algorithm:add_decoy_peptides
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57 #end if
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58 #if $adv_opts.adv_opts_selector=='advanced':
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59 #if $adv_opts.param_force:
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60 -force
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61 #end if
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62 #end if
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63 </command>
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64 <inputs>
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65 <param name="param_in" type="data" format="idxml" optional="False" label="Identifications from searching a target-decoy database" help="(-in) "/>
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66 <param name="param_PSM" display="radio" type="select" optional="False" value="true" label="Perform FDR calculation on PSM level" help="(-PSM) ">
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67 <option value="true" selected="true">true</option>
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68 <option value="false">false</option>
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69 </param>
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70 <param name="param_protein" display="radio" type="select" optional="False" value="true" label="Perform FDR calculation on protein level" help="(-protein) ">
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71 <option value="true" selected="true">true</option>
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72 <option value="false">false</option>
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73 </param>
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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)"/>
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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)"/>
0
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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) "/>
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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) "/>
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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) "/>
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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) "/>
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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"/>
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81 <expand macro="advanced_options">
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82 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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83 </expand>
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84 </inputs>
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85 <outputs>
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86 <data name="param_out" format="idxml"/>
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87 </outputs>
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88 <help>Estimates the false discovery rate on peptide and protein level using decoy searches.
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89
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90
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91 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FalseDiscoveryRate.html</help>
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92 </tool>