Mercurial > repos > galaxyp > openms_falsediscoveryrate

annotate FalseDiscoveryRate.xml @ 15:6ccbf9a2072c draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:02:41 +0000
parents 469690558892
children 4138acdeedfb
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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="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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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="requirements"/>
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11 <expand macro="stdio"/>
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12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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13 @EXT_FOO@
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14 #import re
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16 ## Preprocessing
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17 mkdir in &&
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18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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19 mkdir out &&
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21 ## Main program call
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23 set -o pipefail &&
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24 @EXECUTABLE@ -write_ctd ./ &&
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25 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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26 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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27 -in
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28 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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29 -out
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30 'out/output.${gxy2omsext("idxml")}'
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31
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32 ## Postprocessing
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33 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
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34 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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35 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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36 #end if]]></command>
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37 <configfiles>
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38 <inputs name="args_json" data_style="paths"/>
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39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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40 </configfiles>
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41 <inputs>
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42 <param argument="-in" type="data" format="idxml" optional="false" label="Identifications from searching a target-decoy database" help=" select idxml data sets(s)"/>
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43 <param argument="-PSM" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Perform FDR calculation on PSM level" help=""/>
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44 <param argument="-protein" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Perform FDR calculation on protein level" help=""/>
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45 <section name="FDR" title="FDR control" help="" expanded="false">
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46 <param name="PSM" argument="-FDR:PSM" type="float" optional="true" min="0.0" max="1.0" value="1.0" label="Filter PSMs based on q-value" help="(e.g., 0.05 = 5% FDR, disabled for 1)"/>
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47 <param name="protein" argument="-FDR:protein" type="float" optional="true" min="0.0" max="1.0" value="1.0" label="Filter proteins based on q-value" help="(e.g., 0.05 = 5% FDR, disabled for 1)"/>
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48 <section name="cleanup" title="Cleanup references after FDR control" help="" expanded="false">
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49 <param name="remove_proteins_without_psms" argument="-FDR:cleanup:remove_proteins_without_psms" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Remove proteins without PSMs (due to being decoy or below PSM FDR threshold)" help=""/>
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50 <param name="remove_psms_without_proteins" argument="-FDR:cleanup:remove_psms_without_proteins" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Remove PSMs without proteins (due to being decoy or below protein FDR threshold)" help=""/>
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51 <param name="remove_spectra_without_psms" argument="-FDR:cleanup:remove_spectra_without_psms" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Remove spectra without PSMs (due to being decoy or below protein FDR threshold)" help="Caution: if remove_psms_without_proteins is false, protein level filtering does not propagate"/>
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52 </section>
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53 </section>
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54 <section name="algorithm" title="Parameter section for the FDR calculation algorithm" help="" expanded="false">
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55 <param name="no_qvalues" argument="-algorithm:no_qvalues" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If 'true' strict FDRs will be calculated instead of q-values (the default)" help=""/>
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56 <param name="use_all_hits" argument="-algorithm:use_all_hits" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If 'true' not only the first hit, but all are used (peptides only)" help=""/>
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57 <param name="split_charge_variants" argument="-algorithm:split_charge_variants" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If 'true' charge variants are treated separately (for peptides of combined target/decoy searches only)" help=""/>
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58 <param name="treat_runs_separately" argument="-algorithm:treat_runs_separately" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If 'true' different search runs are treated separately (for peptides of combined target/decoy searches only)" help=""/>
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59 <param name="add_decoy_peptides" argument="-algorithm:add_decoy_peptides" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If 'true' decoy peptides will be written to output file, too" help="The q-value is set to the closest target score"/>
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60 <param name="add_decoy_proteins" argument="-algorithm:add_decoy_proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If 'true' decoy proteins will be written to output file, too" help="The q-value is set to the closest target score"/>
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61 <param name="conservative" argument="-algorithm:conservative" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If 'true' (D+1)/T instead of (D+1)/(T+D) is used as a formula" help=""/>
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62 </section>
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63 <expand macro="adv_opts_macro">
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64 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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65 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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66 <expand macro="list_string_san" name="test"/>
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67 </param>
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68 </expand>
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69 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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70 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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71 </param>
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72 </inputs>
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73 <outputs>
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74 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
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75 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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76 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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77 </data>
0
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78 </outputs>
15
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79 <tests><!-- TOPP_FalseDiscoveryRate_1 -->
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80 <test expect_num_outputs="2">
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81 <section name="adv_opts">
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82 <param name="force" value="false"/>
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83 <param name="test" value="true"/>
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84 </section>
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85 <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
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86 <output name="out" file="FalseDiscoveryRate_output_1.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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87 <param name="PSM" value="true"/>
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88 <param name="protein" value="false"/>
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89 <section name="FDR">
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90 <param name="PSM" value="1.0"/>
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91 <param name="protein" value="1.0"/>
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92 <section name="cleanup">
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93 <param name="remove_proteins_without_psms" value="true"/>
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94 <param name="remove_psms_without_proteins" value="true"/>
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95 <param name="remove_spectra_without_psms" value="true"/>
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96 </section>
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97 </section>
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98 <section name="algorithm">
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99 <param name="no_qvalues" value="false"/>
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100 <param name="use_all_hits" value="false"/>
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101 <param name="split_charge_variants" value="false"/>
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102 <param name="treat_runs_separately" value="false"/>
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103 <param name="add_decoy_peptides" value="false"/>
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104 <param name="add_decoy_proteins" value="false"/>
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105 <param name="conservative" value="true"/>
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106 </section>
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107 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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108 <output name="ctd_out" ftype="xml">
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109 <assert_contents>
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110 <is_valid_xml/>
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111 </assert_contents>
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112 </output>
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113 </test>
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114 <!-- TOPP_FalseDiscoveryRate_2 -->
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115 <test expect_num_outputs="2">
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116 <section name="adv_opts">
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117 <param name="force" value="false"/>
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118 <param name="test" value="true"/>
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119 </section>
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120 <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
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121 <output name="out" file="FalseDiscoveryRate_output_2.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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122 <param name="PSM" value="true"/>
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123 <param name="protein" value="false"/>
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124 <section name="FDR">
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125 <param name="PSM" value="1.0"/>
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126 <param name="protein" value="1.0"/>
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127 <section name="cleanup">
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128 <param name="remove_proteins_without_psms" value="true"/>
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129 <param name="remove_psms_without_proteins" value="true"/>
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130 <param name="remove_spectra_without_psms" value="true"/>
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131 </section>
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132 </section>
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133 <section name="algorithm">
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134 <param name="no_qvalues" value="false"/>
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135 <param name="use_all_hits" value="false"/>
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136 <param name="split_charge_variants" value="false"/>
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137 <param name="treat_runs_separately" value="true"/>
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138 <param name="add_decoy_peptides" value="false"/>
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139 <param name="add_decoy_proteins" value="false"/>
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140 <param name="conservative" value="true"/>
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141 </section>
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142 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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143 <output name="ctd_out" ftype="xml">
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144 <assert_contents>
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145 <is_valid_xml/>
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146 </assert_contents>
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147 </output>
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148 </test>
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149 <!-- TOPP_FalseDiscoveryRate_3 -->
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150 <test expect_num_outputs="2">
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151 <section name="adv_opts">
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152 <param name="force" value="false"/>
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153 <param name="test" value="true"/>
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154 </section>
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155 <param name="in" value="FalseDiscoveryRate_OMSSA.idXML"/>
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156 <output name="out" file="FalseDiscoveryRate_output_3.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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157 <param name="PSM" value="true"/>
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158 <param name="protein" value="false"/>
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159 <section name="FDR">
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160 <param name="PSM" value="1.0"/>
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161 <param name="protein" value="1.0"/>
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162 <section name="cleanup">
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163 <param name="remove_proteins_without_psms" value="true"/>
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164 <param name="remove_psms_without_proteins" value="true"/>
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165 <param name="remove_spectra_without_psms" value="true"/>
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166 </section>
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167 </section>
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168 <section name="algorithm">
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169 <param name="no_qvalues" value="false"/>
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170 <param name="use_all_hits" value="false"/>
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171 <param name="split_charge_variants" value="true"/>
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172 <param name="treat_runs_separately" value="false"/>
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173 <param name="add_decoy_peptides" value="false"/>
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174 <param name="add_decoy_proteins" value="false"/>
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175 <param name="conservative" value="true"/>
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176 </section>
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177 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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178 <output name="ctd_out" ftype="xml">
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179 <assert_contents>
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180 <is_valid_xml/>
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181 </assert_contents>
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182 </output>
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183 </test>
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184 <!-- TOPP_FalseDiscoveryRate_4 -->
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185 <test expect_num_outputs="2">
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186 <section name="adv_opts">
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187 <param name="force" value="false"/>
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188 <param name="test" value="true"/>
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189 </section>
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190 <param name="in" value="FalseDiscoveryRate_OMSSA_4.idXML"/>
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191 <output name="out" file="FalseDiscoveryRate_output_4.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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192 <param name="PSM" value="true"/>
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193 <param name="protein" value="false"/>
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194 <section name="FDR">
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195 <param name="PSM" value="1.0"/>
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196 <param name="protein" value="1.0"/>
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197 <section name="cleanup">
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198 <param name="remove_proteins_without_psms" value="true"/>
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199 <param name="remove_psms_without_proteins" value="true"/>
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200 <param name="remove_spectra_without_psms" value="true"/>
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201 </section>
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202 </section>
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203 <section name="algorithm">
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204 <param name="no_qvalues" value="false"/>
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205 <param name="use_all_hits" value="false"/>
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206 <param name="split_charge_variants" value="true"/>
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207 <param name="treat_runs_separately" value="false"/>
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208 <param name="add_decoy_peptides" value="false"/>
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209 <param name="add_decoy_proteins" value="false"/>
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210 <param name="conservative" value="true"/>
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211 </section>
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212 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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213 <output name="ctd_out" ftype="xml">
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214 <assert_contents>
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215 <is_valid_xml/>
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216 </assert_contents>
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217 </output>
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218 </test>
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219 <!-- TOPP_FalseDiscoveryRate_5 -->
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220 <test expect_num_outputs="2">
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221 <section name="adv_opts">
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222 <param name="force" value="true"/>
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223 <param name="test" value="true"/>
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224 </section>
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225 <param name="in" value="FalseDiscoveryRate_5_input.idXML"/>
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226 <output name="out" file="FalseDiscoveryRate_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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227 <param name="PSM" value="false"/>
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228 <param name="protein" value="true"/>
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229 <section name="FDR">
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230 <param name="PSM" value="1.0"/>
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231 <param name="protein" value="1.0"/>
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232 <section name="cleanup">
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233 <param name="remove_proteins_without_psms" value="true"/>
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234 <param name="remove_psms_without_proteins" value="true"/>
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235 <param name="remove_spectra_without_psms" value="true"/>
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236 </section>
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237 </section>
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238 <section name="algorithm">
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239 <param name="no_qvalues" value="false"/>
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240 <param name="use_all_hits" value="false"/>
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241 <param name="split_charge_variants" value="false"/>
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242 <param name="treat_runs_separately" value="false"/>
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243 <param name="add_decoy_peptides" value="false"/>
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244 <param name="add_decoy_proteins" value="true"/>
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245 <param name="conservative" value="true"/>
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246 </section>
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247 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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248 <output name="ctd_out" ftype="xml">
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249 <assert_contents>
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250 <is_valid_xml/>
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251 </assert_contents>
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252 </output>
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253 </test>
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254 <!-- TOPP_FalseDiscoveryRate_6 -->
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255 <test expect_num_outputs="2">
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256 <section name="adv_opts">
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257 <param name="force" value="false"/>
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258 <param name="test" value="true"/>
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259 </section>
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260 <param name="in" value="FalseDiscoveryRate_6_input.idXML"/>
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261 <output name="out" file="FalseDiscoveryRate_6_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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262 <param name="PSM" value="true"/>
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263 <param name="protein" value="false"/>
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264 <section name="FDR">
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265 <param name="PSM" value="0.05"/>
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266 <param name="protein" value="1.0"/>
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267 <section name="cleanup">
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268 <param name="remove_proteins_without_psms" value="true"/>
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269 <param name="remove_psms_without_proteins" value="true"/>
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270 <param name="remove_spectra_without_psms" value="true"/>
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271 </section>
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272 </section>
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273 <section name="algorithm">
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274 <param name="no_qvalues" value="false"/>
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275 <param name="use_all_hits" value="false"/>
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276 <param name="split_charge_variants" value="false"/>
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277 <param name="treat_runs_separately" value="false"/>
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278 <param name="add_decoy_peptides" value="false"/>
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279 <param name="add_decoy_proteins" value="false"/>
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280 <param name="conservative" value="true"/>
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281 </section>
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282 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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283 <output name="ctd_out" ftype="xml">
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284 <assert_contents>
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285 <is_valid_xml/>
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286 </assert_contents>
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287 </output>
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288 </test>
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289 <!-- TOPP_FalseDiscoveryRate_7 -->
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290 <test expect_num_outputs="2">
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291 <section name="adv_opts">
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292 <param name="force" value="true"/>
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293 <param name="test" value="true"/>
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294 </section>
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295 <param name="in" value="FalseDiscoveryRate_7_input.idXML"/>
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296 <output name="out" file="FalseDiscoveryRate_7_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
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297 <param name="PSM" value="false"/>
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298 <param name="protein" value="true"/>
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299 <section name="FDR">
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300 <param name="PSM" value="1.0"/>
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301 <param name="protein" value="0.3"/>
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302 <section name="cleanup">
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303 <param name="remove_proteins_without_psms" value="true"/>
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304 <param name="remove_psms_without_proteins" value="true"/>
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305 <param name="remove_spectra_without_psms" value="true"/>
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306 </section>
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307 </section>
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308 <section name="algorithm">
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309 <param name="no_qvalues" value="false"/>
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310 <param name="use_all_hits" value="false"/>
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311 <param name="split_charge_variants" value="false"/>
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312 <param name="treat_runs_separately" value="false"/>
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313 <param name="add_decoy_peptides" value="false"/>
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314 <param name="add_decoy_proteins" value="false"/>
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315 <param name="conservative" value="true"/>
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316 </section>
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317 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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318 <output name="ctd_out" ftype="xml">
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319 <assert_contents>
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320 <is_valid_xml/>
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321 </assert_contents>
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322 </output>
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323 </test>
11
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324 </tests>
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325 <help><![CDATA[Estimates the false discovery rate on peptide and protein level using decoy searches.
0
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326
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327
15
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328 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FalseDiscoveryRate.html]]></help>
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100359fb8e7c "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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329 <expand macro="references"/>
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7e4bc43844e3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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330 </tool>