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1 <?xml version="1.0"?>
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2 <tool id="idpqonvert" version="0.1.0" name="idpQonvert" >
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3 <requirements>
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4 <requirement type="package" version="333">binaries_for_package_idpqonvert</requirement>
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5 </requirements>
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6
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7 <!-- TODO: Set defaults for weights correctly -->
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8 <description>
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9 Prepare identification results for IDPicker.
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10 </description>
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11 <command>
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12 #set $db_name = $input_database.display_name.replace(".fasta", "") + ".fasta"
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13 #set $input_name = $input.display_name
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14 #set $output_name = $input_name.split(".")[0] + ".idpDB"
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15 ln -s '$input' '${input_name}';
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16 ln -s '$input_database' '${db_name}';
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17 idpQonvert -DecoyPrefix '${decoy_prefix}' \
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18 -WriteQonversionDetails true \
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19 -ProteinDatabase '${db_name}' \
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20 -MaxFDR $max_fdr \
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21 -EmbedSpectrumScanTimes false \
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22 -EmbedSpectrumSources false \
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23 #if $scoring.override_scoring
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24 #set $score_info = []
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25 #for $engine in ["myrimatch:mvh", "xcorr", "sequest:xcorr", "sequest:deltacn", "mascot:score", "x!tandem:expect", "x!tandem:hyperscore", "ms-gf:spacevalue"]
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26 #set $weight = $getVar("scoring." + $engine.replace(":", "_").replace("!","") + "_weight.value")
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27 #set $type = $getVar("scoring." + $engine.replace(":", "_").replace("!","") + "_type.value")
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28 #set $score_info = $score_info + [str($weight) + " " + $type + " " + $engine]
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29 #continue
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30 #end for
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31 #set $score_str = "; ".join($score_info)
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32 -ScoreInfo '$score_str' \
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33 #end if
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34 #if $advanced_options.use_advanced_options
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35 -MaxImportFDR $advanced_options.max_import_fdr \
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36 -MaxResultRank $advanced_options.max_result_rank \
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37 -RerankMatches $advanced_options.rerank_matches \
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38 -Gamma $advanced_options.gamma \
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39 -Nu $advanced_options.nu \
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40 -PolynomialDegree $advanced_options.polynomial_degree \
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41 -TruePositiveThreshold $advanced_options.true_positive_threshold \
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42 -MaxTrainingRank $advanced_options.max_training_rank \
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43 -SVMType $advanced_options.svm_type \
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44 -Kernel $advanced_options.kernel \
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45 -ChargeStateHandling $advanced_options.charge_state_handling \
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46 -QonverterMethod $advanced_options.qonverter_method \
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47 -MinPartitionSize $advanced_options.min_partition_size \
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48 #end if
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49 '${input_name}';
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50 mv '$output_name' output
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51 </command>
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52 <!-- idpQonvert needs spectrum available EmbedSpectrumScanTimes or EmbedSpectrumSources is set.
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53 -->
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54 <stdio>
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55 <exit_code range="1:" level="fatal" description="Job Failed" />
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56 <regex match="^Could not find the default configuration file.*$"
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57 source="both"
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58 level="warning" />
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59 </stdio>
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60 <inputs>
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61 <conditional name="type">
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62 <param name="input_type" type="select" label="Input Type">
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63 <option value="mzid">mzIdentML</option>
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64 <option value="pepXML">pepXML</option>
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65 </param>
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66 <when value="mzid">
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67 <param format="mzid" name="input" type="data" label="Input mzIdentML"/>
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68 </when>
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69 <when value="pepXML">
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70 <param format="pepXML" name="input" type="data" label="Input pepXML"/>
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71 </when>
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72 </conditional>
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73 <param format="fasta" name="input_database" type="data" label="Protein Database"/>
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74 <param name="decoy_prefix" type="text" label="Decoy Prefix"/>
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75 <param name="max_fdr" type="float" label="Max FDR" value="0.05" />
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76 <conditional name="advanced_options">
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77 <param name="use_advanced_options" type="boolean" truevalue="true" falsevalue="false" label="Set Advanced Options" />
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78 <when value="false" />
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79 <when value="true">
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80 <param name="max_import_fdr" type="float" label="Max Import FDR" value="0.25" />
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81 <param name="max_result_rank" type="integer" label="Max Result Rank" value="3" />
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82 <param name="max_training_rank" type="integer" label="Max Training Rank" value="1" />
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83 <param name="rerank_matches" type="boolean" label="Rerank Matches" checked="false" truevalue="true" falsevalue="false" />
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84 <param name="gamma" type="float" label="Gamma" value="5" />
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85 <param name="nu" type="float" label="Nu" value="-0.5" />
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86 <param name="true_positive_threshold" type="float" label="True Positive Threshold" value="0.01" />
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87 <param name="polynomial_degree" type="integer" label="Polynomial Degree" value="3" />
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88 <param name="min_partition_size" type="integer" label="Minimum Partition Size" value="10" />
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89 <param name="svm_type" label="SVM Type" type="select">
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90 <option value="CSVC" selected="true">CSVC</option>
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91 <option value="NuSVC">Nu SCV</option>
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92 <option value="OneClass">One Class</option>
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93 <option value="NuSVR">Nu SVR</option>
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94 <option value="EpsilonSVR">Epsilon SVR</option>
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95 </param>
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96 <param name="kernel" label="Kernel" type="select">
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97 <option value="Linear" selected="true">Linear</option>
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98 <option value="Polynomial">Polynomial</option>
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99 <option value="RBR">Radial Basis Function</option>
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100 <option value="Sigmoid">Sigmoid</option>
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101 </param>
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102 <param name="charge_state_handling" label="Charge State Handling" type="select">
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103 <option value="Partition" selected="true">Partition</option>
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104 <option value="Ignore">Ignore</option>
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105 <option value="Feature">Feature</option>
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106 </param>
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107 <param name="terminal_specificity_handling" label="Terminal Specificity Handling" type="select">
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108 <option value="Partition" selected="true">Partition</option>
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109 <option value="Ignore">Ignore</option>
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110 <option value="Feature">Feature</option>
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111 </param>
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112 <param name="missed_cleavages_handling" label="Missed Cleavages Handling" type="select">
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113 <option value="Ignore" selected="true">Ignore</option>
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114 <option value="Feature">Feature</option>
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115 </param>
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116 <param name="missed_cleavages_handling" label="Missed Cleavages Handling" type="select">
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117 <option value="Ignore" selected="true">Ignore</option>
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118 <option value="Feature">Feature</option>
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119 </param>
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120 <param name="mass_error_handling" label="Mass Error Handling" type="select">
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121 <option value="Ignore" selected="true">Ignore</option>
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122 <option value="Feature">Feature</option>
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123 </param>
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124 <param name="qonverter_method" label="Qonverter Method" type="select">
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125 <option value="MonteCarlo" selected="true">Monte Carlo</option>
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126 <option value="SingleSVM">SVM (single)</option>
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127 <option value="PartitionSVM">SVM (parition)</option>
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128 <option value="StaticWeighted">Static Weighted</option>
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129 </param>
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130 </when>
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131 </conditional>
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132 <conditional name="scoring">
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133 <param name="override_scoring" type="boolean" truevalue="true" falsevalue="false" label="Modify Search Application Weights" />
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134 <when value="false" />
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135 <when value="true">
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136 <param name="myrimatch_mvh_weight" label="Myrimatch (mvh) Weight" type="float" value="1" />
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137 <param name="myrimatch_mvh_type" label="Myrimatch (mvh) Normalization" type="select">
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138 <option value="off" selected="true">None</option>
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139 <option value="quantile">Quantile</option>
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140 <option value="linear">Linear</option>
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141 </param>
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142 <param name="xcorr_weight" label="XCorr Weight" type="float" value="1" />
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143 <param name="xcorr_type" label="XCorr Normalization" type="select">
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144 <option value="off" selected="true">None</option>
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145 <option value="quantile">Quantile</option>
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146 <option value="linear">Linear</option>
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147 </param>
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148 <param name="sequest_xcorr_weight" label="Sequest (xcorr) Weight" type="float" value="1" />
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149 <param name="sequest_xcorr_type" label="Sequest (xcorr) Normalization" type="select">
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150 <option value="off" selected="true">None</option>
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151 <option value="quantile">Quantile</option>
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152 <option value="linear">Linear</option>
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153 </param>
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154 <param name="sequest_deltacn_weight" label="Sequest (deltacn) Weight" type="float" value="1" />
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155 <param name="sequest_deltacn_type" label="Sequest (deltacn) Normalization" type="select">
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156 <option value="off" selected="true">None</option>
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157 <option value="quantile">Quantile</option>
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158 <option value="linear">Linear</option>
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159 </param>
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160 <param name="mascot_score_weight" label="Mascot Score Weight" type="float" value="1" />
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161 <param name="mascot_score_type" label="Mascot Score Normalization" type="select">
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162 <option value="off" selected="true">None</option>
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163 <option value="quantile">Quantile</option>
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164 <option value="linear">Linear</option>
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165 </param>
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166 <param name="xtandem_expect_weight" label="X! Tandem (Expectation) Weight" type="float" value="-1" />
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167 <param name="xtandem_expect_type" label="X! Tandem (Expectation) Normalization" type="select">
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168 <option value="off" selected="true">None</option>
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169 <option value="quantile">Quantile</option>
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170 <option value="linear">Linear</option>
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171 </param>
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172 <param name="xtandem_hyperscore_weight" label="X! Tandem (hyperscore) Weight" type="float" value="1" />
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173 <param name="xtandem_hyperscore_type" label="X! Tandem (hyperscore)Normalization" type="select">
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174 <option value="off" selected="true">None</option>
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175 <option value="quantile">Quantile</option>
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176 <option value="linear">Linear</option>
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177 </param>
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178 <param name="ms-gf_spacevalue_weight" label="MS-GF (spacevalue) Weight" type="float" value="-1" />
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179 <param name="ms-gf_spacevalue_type" label="MS-GF (spacevalue) Normalization" type="select">
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180 <option value="off" selected="true">None</option>
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181 <option value="quantile">Quantile</option>
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182 <option value="linear">Linear</option>
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183 </param>
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184 </when>
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185 </conditional>
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186 </inputs>
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187 <outputs>
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188 <data format="idpdb" name="output" from_work_dir="output" />
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189 </outputs>
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190 <help>
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191 </help>
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192 </tool>
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193 <!-- idpQonvert needs spectrum available EmbedSpectrumScanTimes or EmbedSpectrumSources is set.
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194
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195 idpQonvert -OverwriteExistingFiles true -MaxFDR 0.05 -MaxImportFDR 0.25 -MaxResultRank 3 -RerankMatches false -TruePositiveThreshold 0.01 -MaxTrainingRank 1 -Gamma 5 -Nu -0.5 -PolynomialDegree 3 -ScoreInfo "1 off myrimatch:mvh; 1 off xcorr; 1 off sequest:xcorr; 1 off sequest:deltacn; 1 off mascot:score; -1 off xexpect; 1 off x\!tandem:hyperscore; -1 off ms-gf:specevalue" -SVMType CSVC -Kernel Linear -ChargeStateHandling Partition -QonverterMethod MonteCarlo -MinPartitionSize 10 -DecoyPrefix RRRRRR -ProteinDatabase test2.fasta input.pepXML
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196
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197
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198 ScoreInfo: 1 off myrimatch:mvh; 1 off xcorr; 1 off sequest:xcorr; 1 off sequest:deltacn; 1 off mascot:score; -1 off x!tandem:expect; 1 off x!tandem:hyperscore; -1 off ms-gf:specevalue
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199
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200 off is normalization: quantile, linear, or off
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201
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202 SVMType: CSVC, NuSVC, OneClass, EpsilonSVR, NuSVR
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203 Kernel: Linear, Polynomial, RBF (radial basis function), Sigmoid
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204 ChargeStateHandling: Parition, Ignore, Feature
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205 TerminalSpecificityHandling: Partition, Ignore, Feature
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206 MissedCleavagesHandling: Ignore, Feature
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207 MassErrorHandling: Ignore, Feature
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208 QonverterMethod: MonteCarlo, SingleSVM, PartitionedSVM, StaticWeighted
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209
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210 -->
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