annotate FalseDiscoveryRate.xml @ 1:e37e8ba1b4b7 draft

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author bgruening
date Thu, 16 Apr 2015 09:01:52 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="2.0.0">
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3 <description>Estimates the false discovery rate on peptide and protein level using decoy searches.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">FalseDiscoveryRate</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>FalseDiscoveryRate
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11
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12 #if $param_in:
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13 -in $param_in
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14 #end if
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15 #if $param_fwd_in:
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16 -fwd_in $param_fwd_in
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17 #end if
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18 #if $param_rev_in:
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19 -rev_in $param_rev_in
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20 #end if
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21 #if $param_out:
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22 -out $param_out
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23 #end if
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24 #if $param_proteins_only:
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25 -proteins_only
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26 #end if
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27 #if $param_peptides_only:
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28 -peptides_only
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29 #end if
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30 -threads \${GALAXY_SLOTS:-24}
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31 #if $param_algorithm_q_value:
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32 -algorithm:q_value
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33 #end if
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34 #if $param_algorithm_use_all_hits:
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35 -algorithm:use_all_hits
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36 #end if
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37 #if $param_algorithm_split_charge_variants:
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38 -algorithm:split_charge_variants
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39 #end if
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40 #if $param_algorithm_treat_runs_separately:
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41 -algorithm:treat_runs_separately
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42 #end if
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43 #if $param_algorithm_decoy_string:
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44 -algorithm:decoy_string "$param_algorithm_decoy_string"
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45 #end if
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46 #if $param_algorithm_add_decoy_peptides:
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47 -algorithm:add_decoy_peptides
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48 #end if
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49 #if $adv_opts.adv_opts_selector=='advanced':
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50 #if $adv_opts.param_force:
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51 -force
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52 #end if
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53 #end if
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54 </command>
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55 <inputs>
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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"/>
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57 <param name="param_fwd_in" type="data" format="idxml" optional="True" label="Identification input to estimate FDR, forward run" help="(-fwd_in) "/>
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58 <param name="param_rev_in" type="data" format="idxml" optional="True" label="Identification input to estimate FDR, decoy run" help="(-rev_in) "/>
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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) "/>
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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) "/>
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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) "/>
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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) "/>
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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) "/>
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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) "/>
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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) ">
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66 <sanitizer>
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67 <valid initial="string.printable">
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68 <remove value="'"/>
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69 <remove value="&quot;"/>
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70 </valid>
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71 </sanitizer>
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72 </param>
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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"/>
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74 <expand macro="advanced_options">
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75 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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76 </expand>
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77 </inputs>
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78 <outputs>
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79 <data name="param_out" format="idxml"/>
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80 </outputs>
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81 <help>**What it does**
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82
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83 Estimates the false discovery rate on peptide and protein level using decoy searches.
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84
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85
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86 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FalseDiscoveryRate.html</help>
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87 <expand macro="references"/>
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88 </tool>