Mercurial > repos > galaxyp > openms_falsediscoveryrate

annotate 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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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 CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [ID Processing]-->
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4 <tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="2.1.0">
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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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14
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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_in_target:
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19 -in_target $param_in_target
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20 #end if
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21 #if $param_in_decoy:
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22 -in_decoy $param_in_decoy
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23 #end if
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24 #if $param_out:
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25 -out $param_out
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26 #end if
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27 #if $param_proteins_only:
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28 -proteins_only
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29 #end if
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30 #if $param_peptides_only:
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31 -peptides_only
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32 #end if
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33 #if $param_algorithm_no_qvalues:
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34 -algorithm:no_qvalues
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35 #end if
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36 #if $param_algorithm_use_all_hits:
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37 -algorithm:use_all_hits
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38 #end if
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39 #if $param_algorithm_split_charge_variants:
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40 -algorithm:split_charge_variants
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41 #end if
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42 #if $param_algorithm_treat_runs_separately:
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43 -algorithm:treat_runs_separately
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44 #end if
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45 #if $param_algorithm_add_decoy_peptides:
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46 -algorithm:add_decoy_peptides
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47 #end if
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48 #if $adv_opts.adv_opts_selector=='advanced':
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49 #if $adv_opts.param_force:
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50 -force
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51 #end if
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52 #end if
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53 </command>
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54 <inputs>
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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"/>
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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) "/>
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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) "/>
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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) "/>
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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) "/>
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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) "/>
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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) "/>
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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) "/>
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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) "/>
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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"/>
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65 <expand macro="advanced_options">
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66 <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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67 </expand>
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68 </inputs>
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69 <outputs>
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70 <data name="param_out" format="idxml"/>
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71 </outputs>
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72 <help>Estimates the false discovery rate on peptide and protein level using decoy searches.
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73
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74
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75 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FalseDiscoveryRate.html</help>
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76 </tool>