annotate PercolatorAdapter.xml @ 0:0e7bb87aa55c draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author galaxyp
date Mon, 12 Feb 2018 13:23:13 -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 CTDConverter.-->
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3 <!--Proposed Tool Section: [ID Processing]-->
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4 <tool id="PercolatorAdapter" name="PercolatorAdapter" version="2.3.0">
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5 <description>Facilitate input to Percolator and reintegrate.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">PercolatorAdapter</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>PercolatorAdapter
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14
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15 -in
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16 #for token in $param_in:
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17 $token
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18 #end for
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19 -in_decoy
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20 #for token in $param_in_decoy:
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21 $token
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22 #end for
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23 #if $param_out:
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24 -out $param_out
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25 #end if
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26 #if $param_mzid_out:
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27 -mzid_out $param_mzid_out
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28 #end if
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29 #if $param_enzyme:
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30 -enzyme
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31 #if " " in str($param_enzyme):
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32 "$param_enzyme"
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33 #else
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34 $param_enzyme
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35 #end if
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36 #end if
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37 #if $param_percolator_executable:
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38 -percolator_executable $param_percolator_executable
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39 #end if
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40 #if $param_peptide_level_fdrs:
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41 -peptide-level-fdrs
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42 #end if
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43 #if $param_protein_level_fdrs:
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44 -protein-level-fdrs
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45 #end if
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46 #if $param_weights:
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47 -weights $param_weights
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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_generic_feature_set:
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51 -generic-feature-set
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52 #end if
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53 #if $adv_opts.param_subset_max_train:
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54 -subset-max-train $adv_opts.param_subset_max_train
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55 #end if
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56 #if $adv_opts.param_cpos:
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57 -cpos $adv_opts.param_cpos
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58 #end if
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59 #if $adv_opts.param_cneg:
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60 -cneg $adv_opts.param_cneg
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61 #end if
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62 #if $adv_opts.param_testFDR:
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63 -testFDR $adv_opts.param_testFDR
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64 #end if
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65 #if $adv_opts.param_trainFDR:
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66 -trainFDR $adv_opts.param_trainFDR
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67 #end if
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68 #if $adv_opts.param_maxiter:
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69 -maxiter $adv_opts.param_maxiter
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70 #end if
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71 #if $adv_opts.param_quick_validation:
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72 -quick-validation
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73 #end if
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74 #if $adv_opts.param_init_weights:
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75 -init-weights $adv_opts.param_init_weights
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76 #end if
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77 #if $adv_opts.param_default_direction:
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78 -default-direction "$adv_opts.param_default_direction"
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79 #end if
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80 #if $adv_opts.param_verbose:
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81 -verbose $adv_opts.param_verbose
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82 #end if
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83 #if $adv_opts.param_unitnorm:
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84 -unitnorm
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85 #end if
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86 #if $adv_opts.param_test_each_iteration:
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87 -test-each-iteration
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88 #end if
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89 #if $adv_opts.param_override:
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90 -override
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91 #end if
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92 #if $adv_opts.param_seed:
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93 -seed $adv_opts.param_seed
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94 #end if
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95 #if $adv_opts.param_doc:
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96 -doc $adv_opts.param_doc
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97 #end if
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98 #if $adv_opts.param_klammer:
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99 -klammer
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100 #end if
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101 #if $adv_opts.param_fasta:
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102 -fasta $adv_opts.param_fasta
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103 #end if
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104 #if $adv_opts.param_decoy_pattern:
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105 -decoy-pattern "$adv_opts.param_decoy_pattern"
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106 #end if
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107 #if $adv_opts.param_post_processing_tdc:
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108 -post-processing-tdc
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109 #end if
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110 #if $adv_opts.param_force:
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111 -force
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112 #end if
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113 #end if
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114 </command>
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115 <inputs>
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116 <param name="param_in" type="data" format="mzid,idxml" multiple="true" optional="False" size="30" label="Input file(s)" help="(-in) ">
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117 <sanitizer>
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118 <valid initial="string.printable">
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119 <remove value="'"/>
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120 <remove value="&quot;"/>
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121 </valid>
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122 </sanitizer>
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123 </param>
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124 <param name="param_in_decoy" type="data" format="mzid,idxml" multiple="true" optional="True" size="30" label="Input decoy file(s) in case of separate searches" help="(-in_decoy) ">
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125 <sanitizer>
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126 <valid initial="string.printable">
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127 <remove value="'"/>
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128 <remove value="&quot;"/>
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129 </valid>
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130 </sanitizer>
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131 </param>
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132 <param name="param_enzyme" type="select" optional="False" value="trypsin" label="Type of enzyme: no_enzyme,elastase,pepsin,proteinasek,thermolysin,chymotrypsin,lys-n,lys-c,arg-c,asp-n,glu-c,trypsin" help="(-enzyme) ">
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133 <option value="no_enzyme">no_enzyme</option>
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134 <option value="elastase">elastase</option>
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135 <option value="pepsin">pepsin</option>
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136 <option value="proteinasek">proteinasek</option>
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137 <option value="thermolysin">thermolysin</option>
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138 <option value="chymotrypsin">chymotrypsin</option>
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139 <option value="lys-n">lys-n</option>
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140 <option value="lys-c">lys-c</option>
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141 <option value="arg-c">arg-c</option>
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142 <option value="asp-n">asp-n</option>
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143 <option value="glu-c">glu-c</option>
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144 <option value="trypsin" selected="true">trypsin</option>
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145 </param>
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146 <param name="param_percolator_executable" type="data" format="txt" value="percolator" label="Percolator executable of the installation" help="(-percolator_executable) e.g. 'percolator.exe'"/>
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147 <param name="param_peptide_level_fdrs" display="radio" type="boolean" truevalue="-peptide-level-fdrs" falsevalue="" checked="false" optional="True" label="Calculate peptide-level FDRs instead of PSM-level FDRs" help="(-peptide-level-fdrs) "/>
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148 <param name="param_protein_level_fdrs" display="radio" type="boolean" truevalue="-protein-level-fdrs" falsevalue="" checked="false" optional="True" label="Use the picked protein-level FDR to infer protein probabilities" help="(-protein-level-fdrs) Use the -fasta option and -decoy-pattern to set the Fasta file and decoy pattern"/>
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149 <expand macro="advanced_options">
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150 <param name="param_generic_feature_set" display="radio" type="boolean" truevalue="-generic-feature-set" falsevalue="" checked="false" optional="True" label="Use only generic (i.e" help="(-generic-feature-set) not search engine specific) features. Generating search engine specific features for common search engines by PSMFeatureExtractor will typically boost the identification rate significantly"/>
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151 <param name="param_subset_max_train" type="integer" value="0" label="Only train an SVM on a subset of &lt;x&gt; PSMs, and use the resulting score vector to evaluate the other PSMs" help="(-subset-max-train) Recommended when analyzing huge numbers (&gt;1 million) of PSMs. When set to 0, all PSMs are used for training as normal"/>
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152 <param name="param_cpos" type="float" value="0.0" label="Cpos, penalty for mistakes made on positive examples" help="(-cpos) Set by cross validation if not specified"/>
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153 <param name="param_cneg" type="float" value="0.0" label="Cneg, penalty for mistakes made on negative examples" help="(-cneg) Set by cross validation if not specified"/>
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154 <param name="param_testFDR" type="float" value="0.01" label="False discovery rate threshold for evaluating best cross validation result and the reported end result" help="(-testFDR) "/>
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155 <param name="param_trainFDR" type="float" value="0.01" label="False discovery rate threshold to define positive examples in training" help="(-trainFDR) Set to testFDR if 0"/>
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156 <param name="param_maxiter" type="integer" value="10" label="Maximal number of iterations" help="(-maxiter) "/>
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157 <param name="param_quick_validation" display="radio" type="boolean" truevalue="-quick-validation" falsevalue="" checked="false" optional="True" label="Quicker execution by reduced internal cross-validation" help="(-quick-validation) "/>
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158 <param name="param_init_weights" type="data" format="txt" label="Read initial weights to the given file" help="(-init-weights) "/>
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159 <param name="param_default_direction" type="text" size="30" label="The most informative feature given as the feature name, can be negated to indicate that a lower value is bette" help="(-default-direction) ">
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160 <sanitizer>
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161 <valid initial="string.printable">
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162 <remove value="'"/>
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163 <remove value="&quot;"/>
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164 </valid>
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165 </sanitizer>
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166 </param>
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167 <param name="param_verbose" type="integer" value="2" label="Set verbosity of output: 0=no processing info, 5=all" help="(-verbose) "/>
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168 <param name="param_unitnorm" display="radio" type="boolean" truevalue="-unitnorm" falsevalue="" checked="false" optional="True" label="Use unit normalization [0-1] instead of standard deviation normalization" help="(-unitnorm) "/>
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169 <param name="param_test_each_iteration" display="radio" type="boolean" truevalue="-test-each-iteration" falsevalue="" checked="false" optional="True" label="Measure performance on test set each iteration" help="(-test-each-iteration) "/>
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170 <param name="param_override" display="radio" type="boolean" truevalue="-override" falsevalue="" checked="false" optional="True" label="Override error check and do not fall back on default score vector in case of suspect score vecto" help="(-override) "/>
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171 <param name="param_seed" type="integer" value="1" label="Setting seed of the random number generato" help="(-seed) "/>
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172 <param name="param_doc" type="integer" value="0" label="Include description of correct features" help="(-doc) "/>
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173 <param name="param_klammer" display="radio" type="boolean" truevalue="-klammer" falsevalue="" checked="false" optional="True" label="Retention time features calculated as in Klammer et al" help="(-klammer) Only available if -doc is set"/>
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174 <param name="param_fasta" type="data" format="fasta" optional="True" label="Provide the fasta file as the argument to this flag, which will be used for protein grouping based on an in-silico digest (only valid if option -protein-level-fdrs is active)" help="(-fasta) "/>
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175 <param name="param_decoy_pattern" type="text" size="30" value="random" label="Define the text pattern to identify the decoy proteins and/or PSMs, set this up if the label that identifies the decoys in the database is not the default (Only valid if option -protein-level-fdrs is active)" help="(-decoy-pattern) ">
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176 <sanitizer>
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177 <valid initial="string.printable">
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178 <remove value="'"/>
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179 <remove value="&quot;"/>
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180 </valid>
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181 </sanitizer>
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182 </param>
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183 <param name="param_post_processing_tdc" display="radio" type="boolean" truevalue="-post-processing-tdc" falsevalue="" checked="false" optional="True" label="Use target-decoy competition to assign q-values and PEPs" help="(-post-processing-tdc) "/>
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184 <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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185 </expand>
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186 </inputs>
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187 <outputs>
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188 <data name="param_out" format="idxml"/>
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189 <data name="param_mzid_out" format="mzid"/>
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190 <data name="param_weights" format="data"/>
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191 </outputs>
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192 <help>Facilitate input to Percolator and reintegrate.
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193
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194
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195 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PercolatorAdapter.html</help>
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196 </tool>