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1 <tool id="idpQonvert" name="idpQonvert" version="0.1.0">
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2 <!-- TODO: Set defaults for weights correctly -->
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3 <description>
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4 Prepare identification results for IDPicker.
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5 </description>
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6 <command>
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7 #set $db_name = $input_database.display_name.replace(".fasta", "") + ".fasta"
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8 #set $input_name = $input.display_name
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9 #set $output_name = $input_name.split(".")[0] + ".idpDB"
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10 ln -s '$input' '${input_name}';
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11 ln -s '$input_database' '${db_name}';
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12 idpQonvert -DecoyPrefix '${decoy_prefix}' \
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13 -WriteQonversionDetails true \
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14 -ProteinDatabase '${db_name}' \
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15 -MaxFDR $max_fdr \
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16 -EmbedSpectrumScanTimes false \
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17 -EmbedSpectrumSources false \
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18 #if $scoring.override_scoring
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19 #set $score_info = []
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20 #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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21 #set $weight = $getVar("scoring." + $engine.replace(":", "_").replace("!","") + "_weight.value")
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22 #set $type = $getVar("scoring." + $engine.replace(":", "_").replace("!","") + "_type.value")
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23 #set $score_info = $score_info + [str($weight) + " " + $type + " " + $engine]
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24 #continue
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25 #end for
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26 #set $score_str = "; ".join($score_info)
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27 -ScoreInfo '$score_str' \
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28 #end if
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29 #if $advanced_options.use_advanced_options
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30 -MaxImportFDR $advanced_options.max_import_fdr \
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31 -MaxResultRank $advanced_options.max_result_rank \
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32 -RerankMatches $advanced_options.rerank_matches \
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33 -Gamma $advanced_options.gamma \
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34 -Nu $advanced_options.nu \
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35 -PolynomialDegree $advanced_options.polynomial_degree \
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36 -TruePositiveThreshold $advanced_options.true_positive_threshold \
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37 -MaxTrainingRank $advanced_options.max_training_rank \
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38 -SVMType $advanced_options.svm_type \
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39 -Kernel $advanced_options.kernel \
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40 -ChargeStateHandling $advanced_options.charge_state_handling \
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41 -QonverterMethod $advanced_options.qonverter_method \
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42 -MinPartitionSize $advanced_options.min_partition_size \
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43 #end if
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44 '${input_name}';
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45 mv '$output_name' output
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46 </command>
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47 <!-- idpQonvert needs spectrum available EmbedSpectrumScanTimes or EmbedSpectrumSources is set.
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48 -->
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49 <stdio>
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50 <exit_code range="1:" level="fatal" description="Job Failed" />
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51 <regex match="^Could not find the default configuration file.*$"
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52 source="both"
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53 level="warning" />
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54 </stdio>
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55 <inputs>
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56 <conditional name="type">
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57 <param name="input_type" type="select" label="Input Type">
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58 <option value="mzid">mzIdentML</option>
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59 <option value="pepXML">pepXML</option>
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60 </param>
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61 <when value="mzid">
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62 <param format="mzid" name="input" type="data" label="Input mzIdentML"/>
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63 </when>
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64 <when value="pepXML">
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65 <param format="pepXML" name="input" type="data" label="Input pepXML"/>
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66 </when>
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67 </conditional>
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68 <param format="fasta" name="input_database" type="data" label="Protein Database"/>
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69 <param name="decoy_prefix" type="text" label="Decoy Prefix"/>
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70 <param name="max_fdr" type="float" label="Max FDR" value="0.05" />
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71 <conditional name="advanced_options">
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72 <param name="use_advanced_options" type="boolean" truevalue="true" falsevalue="false" label="Set Advanced Options" help="" />
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73 <when value="false" />
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74 <when value="true">
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75 <param name="max_import_fdr" type="float" label="Max Import FDR" value="0.25" />
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76 <param name="max_result_rank" type="integer" label="Max Result Rank" value="3" />
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77 <param name="max_training_rank" type="integer" label="Max Training Rank" value="1" />
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78 <param name="rerank_matches" type="boolean" label="Rerank Matches" checked="false" truevalue="true" falsevalue="false" />
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79 <param name="gamma" type="float" label="Gamma" value="5" />
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80 <param name="nu" type="float" label="Nu" value="-0.5" />
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81 <param name="true_positive_threshold" type="float" label="True Positive Threshold" value="0.01" />
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82 <param name="polynomial_degree" type="integer" label="Polynomial Degree" value="3" />
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83 <param name="min_partition_size" type="integer" label="Minimum Partition Size" value="10" />
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84 <param name="svm_type" label="SVM Type" type="select">
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85 <option value="CSVC" selected="true">CSVC</option>
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86 <option value="NuSVC">Nu SCV</option>
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87 <option value="OneClass">One Class</option>
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88 <option value="NuSVR">Nu SVR</option>
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89 <option value="EpsilonSVR">Epsilon SVR</option>
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90 </param>
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91 <param name="kernel" label="Kernel" type="select">
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92 <option value="Linear" selected="true">Linear</option>
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93 <option value="Polynomial">Polynomial</option>
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94 <option value="RBR">Radial Basis Function</option>
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95 <option value="Sigmoid">Sigmoid</option>
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96 </param>
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97 <param name="charge_state_handling" label="Charge State Handling" type="select">
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98 <option value="Partition" selected="true">Partition</option>
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99 <option value="Ignore">Ignore</option>
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100 <option value="Feature">Feature</option>
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101 </param>
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102 <param name="terminal_specificity_handling" label="Terminal Specificity 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="missed_cleavages_handling" label="Missed Cleavages Handling" type="select">
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108 <option value="Ignore" selected="true">Ignore</option>
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109 <option value="Feature">Feature</option>
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110 </param>
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111 <param name="missed_cleavages_handling" label="Missed Cleavages Handling" type="select">
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112 <option value="Ignore" selected="true">Ignore</option>
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113 <option value="Feature">Feature</option>
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114 </param>
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115 <param name="mass_error_handling" label="Mass Error Handling" type="select">
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116 <option value="Ignore" selected="true">Ignore</option>
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117 <option value="Feature">Feature</option>
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118 </param>
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119 <param name="qonverter_method" label="Qonverter Method" type="select">
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120 <option value="MonteCarlo" selected="true">Monte Carlo</option>
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121 <option value="SingleSVM">SVM (single)</option>
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122 <option value="PartitionSVM">SVM (parition)</option>
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123 <option value="StaticWeighted">Static Weighted</option>
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124 </param>
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125 </when>
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126 </conditional>
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127 <conditional name="scoring">
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128 <param name="override_scoring" type="boolean" truevalue="true" falsevalue="false" label="Modify Search Application Weights" />
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129 <when value="false" />
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130 <when value="true">
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131 <param name="myrimatch_mvh_weight" label="Myrimatch (mvh) Weight" type="float" value="1" />
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132 <param name="myrimatch_mvh_type" label="Myrimatch (mvh) Normalization" type="select">
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133 <option value="off" selected="true">None</option>
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134 <option value="quantile">Quantile</option>
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135 <option value="linear">Linear</option>
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136 </param>
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137 <param name="xcorr_weight" label="XCorr Weight" type="float" value="1" />
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138 <param name="xcorr_type" label="XCorr Normalization" type="select">
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139 <option value="off" selected="true">None</option>
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140 <option value="quantile">Quantile</option>
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141 <option value="linear">Linear</option>
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142 </param>
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143 <param name="sequest_xcorr_weight" label="Sequest (xcorr) Weight" type="float" value="1" />
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144 <param name="sequest_xcorr_type" label="Sequest (xcorr) Normalization" type="select">
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145 <option value="off" selected="true">None</option>
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146 <option value="quantile">Quantile</option>
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147 <option value="linear">Linear</option>
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148 </param>
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149 <param name="sequest_deltacn_weight" label="Sequest (deltacn) Weight" type="float" value="1" />
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150 <param name="sequest_deltacn_type" label="Sequest (deltacn) Normalization" type="select">
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151 <option value="off" selected="true">None</option>
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152 <option value="quantile">Quantile</option>
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153 <option value="linear">Linear</option>
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154 </param>
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155 <param name="mascot_score_weight" label="Mascot Score Weight" type="float" value="1" />
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156 <param name="mascot_score_type" label="Mascot Score Normalization" type="select">
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157 <option value="off" selected="true">None</option>
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158 <option value="quantile">Quantile</option>
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159 <option value="linear">Linear</option>
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160 </param>
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161 <param name="xtandem_expect_weight" label="X! Tandem (Expectation) Weight" type="float" value="-1" />
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162 <param name="xtandem_expect_type" label="X! Tandem (Expectation) Normalization" type="select">
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163 <option value="off" selected="true">None</option>
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164 <option value="quantile">Quantile</option>
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165 <option value="linear">Linear</option>
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166 </param>
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167 <param name="xtandem_hyperscore_weight" label="X! Tandem (hyperscore) Weight" type="float" value="1" />
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168 <param name="xtandem_hyperscore_type" label="X! Tandem (hyperscore)Normalization" type="select">
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169 <option value="off" selected="true">None</option>
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170 <option value="quantile">Quantile</option>
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171 <option value="linear">Linear</option>
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172 </param>
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173 <param name="ms-gf_spacevalue_weight" label="MS-GF (spacevalue) Weight" type="float" value="-1" />
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174 <param name="ms-gf_spacevalue_type" label="MS-GF (spacevalue) Normalization" type="select">
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175 <option value="off" selected="true">None</option>
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176 <option value="quantile">Quantile</option>
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177 <option value="linear">Linear</option>
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178 </param>
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179 </when>
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180 </conditional>
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181 </inputs>
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182 <outputs>
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183 <data format="idpdb" name="output" from_work_dir="output" />
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184 </outputs>
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185 <requirements>
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186 <requirement type="package" version="3.0.475">idpqonvert</requirement>
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187 </requirements>
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188 <help>
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189 **What it does**
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190
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191 ------
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192
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193 **Citation**
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194
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195 For the underlying tool, please cite `TODO`
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196
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197 If you use this tool in Galaxy, please cite TODO
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198 </help>
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199 </tool>
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200 <!-- idpQonvert needs spectrum available EmbedSpectrumScanTimes or EmbedSpectrumSources is set.
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201
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202 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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203
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204
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205 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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206
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207 off is normalization: quantile, linear, or off
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208
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209 SVMType: CSVC, NuSVC, OneClass, EpsilonSVR, NuSVR
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210 Kernel: Linear, Polynomial, RBF (radial basis function), Sigmoid
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211 ChargeStateHandling: Parition, Ignore, Feature
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212 TerminalSpecificityHandling: Partition, Ignore, Feature
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213 MissedCleavagesHandling: Ignore, Feature
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214 MassErrorHandling: Ignore, Feature
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215 QonverterMethod: MonteCarlo, SingleSVM, PartitionedSVM, StaticWeighted
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216
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217 -->
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