Mercurial > repos > galaxyp > openms_featurefinderidentification

annotate FeatureFinderIdentification.xml @ 3:c040ffc3ac9b draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:54:55 -0400
parents 6a3bbd5b8cb6
children 39ccf2ebfe49
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3a61c78033f0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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 CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Quantitation]-->
3
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4 <tool id="FeatureFinderIdentification" name="FeatureFinderIdentification" version="2.2.0">
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5 <description>Detects features in MS1 data based on peptide identifications.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FeatureFinderIdentification</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>FeatureFinderIdentification
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_id:
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19 -id $param_id
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20 #end if
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21 #if $param_id_ext:
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22 -id_ext $param_id_ext
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23 #end if
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24 #if $param_out:
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25 -out $param_out
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26 #end if
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27 #if $param_lib_out:
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28 -lib_out $param_lib_out
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29 #end if
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30 #if $param_chrom_out:
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31 -chrom_out $param_chrom_out
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32 #end if
3
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33 #if $param_candidates_out:
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34 -candidates_out $param_candidates_out
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35 #end if
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36 #if $param_extract_mz_window:
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37 -extract:mz_window $param_extract_mz_window
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38 #end if
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39 #if $param_extract_n_isotopes:
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40 -extract:n_isotopes $param_extract_n_isotopes
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41 #end if
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42 #if $param_detect_peak_width:
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43 -detect:peak_width $param_detect_peak_width
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44 #end if
3
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45 #if $param_detect_mapping_tolerance:
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46 -detect:mapping_tolerance $param_detect_mapping_tolerance
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47 #end if
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48 #if $param_svm_samples:
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49 -svm:samples $param_svm_samples
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50 #end if
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51 #if $param_svm_no_selection:
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52 -svm:no_selection
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53 #end if
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54 #if $param_svm_xval_out:
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55 -svm:xval_out $param_svm_xval_out
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56 #end if
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57 #if $param_svm_kernel:
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58 -svm:kernel
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59 #if " " in str($param_svm_kernel):
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60 "$param_svm_kernel"
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61 #else
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62 $param_svm_kernel
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63 #end if
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64 #end if
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65 #if $param_svm_xval:
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66 -svm:xval $param_svm_xval
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67 #end if
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68
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69 #if $rep_param_svm_log2_C:
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70 -svm:log2_C
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71 #for token in $rep_param_svm_log2_C:
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72 #if " " in str(token):
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73 "$token.param_svm_log2_C"
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74 #else
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75 $token.param_svm_log2_C
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76 #end if
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77 #end for
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78 #end if
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79
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80 #if $rep_param_svm_log2_gamma:
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81 -svm:log2_gamma
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82 #for token in $rep_param_svm_log2_gamma:
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83 #if " " in str(token):
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84 "$token.param_svm_log2_gamma"
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85 #else
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86 $token.param_svm_log2_gamma
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87 #end if
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88 #end for
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89 #end if
0
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90 #if $param_model_type:
1
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91 -model:type
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92 #if " " in str($param_model_type):
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93 "$param_model_type"
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94 #else
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95 $param_model_type
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96 #end if
0
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97 #end if
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98 #if $adv_opts.adv_opts_selector=='advanced':
3
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99 #if $adv_opts.param_candidates_in:
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100 -candidates_in $adv_opts.param_candidates_in
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101 #end if
0
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102 #if $adv_opts.param_force:
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103 -force
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104 #end if
3
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105 #if $adv_opts.param_extract_isotope_pmin:
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106 -extract:isotope_pmin $adv_opts.param_extract_isotope_pmin
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107 #end if
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108 #if $adv_opts.param_extract_rt_quantile:
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109 -extract:rt_quantile $adv_opts.param_extract_rt_quantile
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110 #end if
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111 #if $adv_opts.param_extract_rt_window:
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112 -extract:rt_window $adv_opts.param_extract_rt_window
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113 #end if
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114 #if $adv_opts.param_detect_min_peak_width:
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115 -detect:min_peak_width $adv_opts.param_detect_min_peak_width
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116 #end if
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117 #if $adv_opts.param_detect_signal_to_noise:
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118 -detect:signal_to_noise $adv_opts.param_detect_signal_to_noise
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119 #end if
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120 #if $adv_opts.param_svm_epsilon:
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121 -svm:epsilon $adv_opts.param_svm_epsilon
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122 #end if
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123 #if $adv_opts.param_svm_cache_size:
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124 -svm:cache_size $adv_opts.param_svm_cache_size
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125 #end if
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126 #if $adv_opts.param_svm_no_shrinking:
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127 -svm:no_shrinking
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128 #end if
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129 #if $adv_opts.param_svm_predictors:
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130 -svm:predictors "$adv_opts.param_svm_predictors"
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131 #end if
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132 #if $adv_opts.param_svm_min_prob:
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133 -svm:min_prob $adv_opts.param_svm_min_prob
0
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134 #end if
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135 #if $adv_opts.param_model_add_zeros:
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136 -model:add_zeros $adv_opts.param_model_add_zeros
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137 #end if
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138 #if $adv_opts.param_model_unweighted_fit:
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139 -model:unweighted_fit
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140 #end if
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141 #if $adv_opts.param_model_no_imputation:
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142 -model:no_imputation
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143 #end if
3
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144 #if $adv_opts.param_model_check_min_area:
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145 -model:check:min_area $adv_opts.param_model_check_min_area
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146 #end if
0
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147 #if $adv_opts.param_model_check_boundaries:
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148 -model:check:boundaries $adv_opts.param_model_check_boundaries
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149 #end if
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150 #if $adv_opts.param_model_check_width:
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151 -model:check:width $adv_opts.param_model_check_width
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152 #end if
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153 #if $adv_opts.param_model_check_asymmetry:
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154 -model:check:asymmetry $adv_opts.param_model_check_asymmetry
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155 #end if
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156 #end if
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157 </command>
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158 <inputs>
3
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159 <param name="param_in" type="data" format="mzml" optional="False" label="Input file: LC-MS raw data" help="(-in) "/>
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160 <param name="param_id" type="data" format="idxml" optional="False" label="Input file: Peptide identifications derived directly from 'in'" help="(-id) "/>
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161 <param name="param_id_ext" type="data" format="idxml" optional="True" label="Input file: 'External' peptide identifications (" help="(-id_ext) e.g. from aligned runs)"/>
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162 <param name="param_extract_mz_window" type="float" min="0.0" optional="True" value="10.0" label="m/z window size for chromatogram extraction (unit: ppm if 1 or greater, else Da/Th)" help="(-mz_window) "/>
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163 <param name="param_extract_n_isotopes" type="integer" min="2" optional="True" value="2" label="Number of isotopes to include in each peptide assay" help="(-n_isotopes) "/>
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164 <param name="param_detect_peak_width" type="float" min="0.0" optional="True" value="60.0" label="Expected elution peak width in seconds, for smoothing (Gauss filter)" help="(-peak_width) Also determines the RT extration window, unless set explicitly via 'extract:rt_window'"/>
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165 <param name="param_detect_mapping_tolerance" type="float" min="0.0" optional="True" value="0.0" label="RT tolerance (plus/minus) for mapping peptide IDs to features" help="(-mapping_tolerance) Absolute value in seconds if 1 or greater, else relative to the RT span of the feature"/>
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166 <param name="param_svm_samples" type="integer" min="0" optional="True" value="0" label="Number of observations to use for training ('0' for all)" help="(-samples) "/>
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167 <param name="param_svm_no_selection" display="radio" type="boolean" truevalue="-svm:no_selection" falsevalue="" checked="false" optional="True" label="By default, roughly the same number of positive and negative observations, with the same intensity distribution, are selected for training" help="(-no_selection) This aims to reduce biases, but also reduces the amount of training data. Set this flag to skip this procedure and consider all available observations (subject to 'svm:samples')"/>
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168 <param name="param_svm_kernel" display="radio" type="select" optional="False" value="RBF" label="SVM kernel" help="(-kernel) ">
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169 <option value="RBF" selected="true">RBF</option>
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170 <option value="linear">linear</option>
0
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171 </param>
3
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172 <param name="param_svm_xval" type="integer" min="1" optional="True" value="5" label="Number of partitions for cross-validation (parameter optimization)" help="(-xval) "/>
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173 <repeat name="rep_param_svm_log2_C" min="0" max="1" title="param_svm_log2_C">
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174 <param name="param_svm_log2_C" type="text" size="30" value="-5.0 -3.0 -1.0 1.0 3.0 5.0 7.0 9.0 11.0 13.0 15.0" label="Values to try for the SVM parameter 'C' during parameter optimization" help="(-log2_C) A value 'x' is used as 'C = 2^x'">
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175 <sanitizer>
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176 <valid initial="string.printable">
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177 <remove value="'"/>
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178 <remove value="&quot;"/>
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179 </valid>
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180 </sanitizer>
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181 </param>
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182 </repeat>
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183 <repeat name="rep_param_svm_log2_gamma" min="0" max="1" title="param_svm_log2_gamma">
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184 <param name="param_svm_log2_gamma" type="text" size="30" value="-15.0 -13.0 -11.0 -9.0 -7.0 -5.0 -3.0 -1.0 1.0 3.0" label="Values to try for the SVM parameter 'gamma' during parameter optimization (RBF kernel only)" help="(-log2_gamma) A value 'x' is used as 'gamma = 2^x'">
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185 <sanitizer>
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186 <valid initial="string.printable">
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187 <remove value="'"/>
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188 <remove value="&quot;"/>
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189 </valid>
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190 </sanitizer>
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191 </param>
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192 </repeat>
0
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193 <param name="param_model_type" display="radio" type="select" optional="False" value="symmetric" label="Type of elution model to fit to features" help="(-type) ">
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194 <option value="symmetric" selected="true">symmetric</option>
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195 <option value="asymmetric">asymmetric</option>
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196 <option value="none">none</option>
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197 </param>
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198 <expand macro="advanced_options">
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199 <param name="param_candidates_in" type="data" format="featurexml" optional="True" label="Input file: Feature candidates from a previous run" help="(-candidates_in) If set, only feature classification and elution model fitting are carried out, if enabled. Many parameters are ignored"/>
0
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200 <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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201 <param name="param_extract_isotope_pmin" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Minimum probability for an isotope to be included in the assay for a peptide" help="(-isotope_pmin) If set, this parameter takes precedence over 'extract:n_isotopes'"/>
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202 <param name="param_extract_rt_quantile" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="Quantile of the RT deviations between aligned internal and external IDs to use for scaling the RT extraction window" help="(-rt_quantile) "/>
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203 <param name="param_extract_rt_window" type="float" min="0.0" optional="True" value="0.0" label="RT window size (in sec.) for chromatogram extraction" help="(-rt_window) If set, this parameter takes precedence over 'extract:rt_quantile'"/>
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204 <param name="param_detect_min_peak_width" type="float" min="0.0" optional="True" value="0.2" label="Minimum elution peak width" help="(-min_peak_width) Absolute value in seconds if 1 or greater, else relative to 'peak_width'"/>
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205 <param name="param_detect_signal_to_noise" type="float" min="0.1" optional="True" value="0.8" label="Signal-to-noise threshold for OpenSWATH feature detection" help="(-signal_to_noise) "/>
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206 <param name="param_svm_epsilon" type="float" min="0.0" optional="True" value="0.001" label="Stopping criterion" help="(-epsilon) "/>
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207 <param name="param_svm_cache_size" type="float" min="1.0" optional="True" value="100.0" label="Size of the kernel cache (in MB)" help="(-cache_size) "/>
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208 <param name="param_svm_no_shrinking" display="radio" type="boolean" truevalue="-svm:no_shrinking" falsevalue="" checked="false" optional="True" label="Disable the shrinking heuristics" help="(-no_shrinking) "/>
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209 <param name="param_svm_predictors" type="text" size="30" value="peak_apices_sum,var_xcorr_coelution,var_xcorr_shape,var_library_sangle,var_intensity_score,sn_ratio,var_log_sn_score,var_elution_model_fit_score,xx_lda_prelim_score,var_isotope_correlation_score,var_isotope_overlap_score,var_massdev_score,main_var_xx_swath_prelim_score" label="Names of OpenSWATH scores to use as predictors for the SVM (comma-separated list)" help="(-predictors) ">
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210 <sanitizer>
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211 <valid initial="string.printable">
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212 <remove value="'"/>
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213 <remove value="&quot;"/>
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214 </valid>
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215 </sanitizer>
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216 </param>
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217 <param name="param_svm_min_prob" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Minimum probability of correctness, as predicted by the SVM, required to retain a feature candidate" help="(-min_prob) "/>
0
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218 <param name="param_model_add_zeros" type="float" min="0.0" optional="True" value="0.2" label="Add zero-intensity points outside the feature range to constrain the model fit" help="(-add_zeros) This parameter sets the weight given to these points during model fitting; '0' to disable"/>
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219 <param name="param_model_unweighted_fit" display="radio" type="boolean" truevalue="-model:unweighted_fit" falsevalue="" checked="false" optional="True" label="Suppress weighting of mass traces according to theoretical intensities when fitting elution models" help="(-unweighted_fit) "/>
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220 <param name="param_model_no_imputation" display="radio" type="boolean" truevalue="-model:no_imputation" falsevalue="" checked="false" optional="True" label="If fitting the elution model fails for a feature, set its intensity to zero instead of imputing a value from the initial intensity estimate" help="(-no_imputation) "/>
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221 <param name="param_model_check_min_area" type="float" min="0.0" optional="True" value="1.0" label="Lower bound for the area under the curve of a valid elution model" help="(-min_area) "/>
0
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222 <param name="param_model_check_boundaries" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Time points corresponding to this fraction of the elution model height have to be within the data region used for model fitting" help="(-boundaries) "/>
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223 <param name="param_model_check_width" type="float" min="0.0" optional="True" value="10.0" label="Upper limit for acceptable widths of elution models (Gaussian or EGH), expressed in terms of modified (median-based) z-scores; '0' to disable" help="(-width) "/>
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224 <param name="param_model_check_asymmetry" type="float" min="0.0" optional="True" value="10.0" label="Upper limit for acceptable asymmetry of elution models (EGH only), expressed in terms of modified (median-based) z-scores; '0' to disable" help="(-asymmetry) "/>
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225 </expand>
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226 </inputs>
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227 <outputs>
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228 <data name="param_out" format="featurexml"/>
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229 <data name="param_lib_out" format="traml"/>
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230 <data name="param_chrom_out" format="mzml"/>
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231 <data name="param_candidates_out" format="featurexml"/>
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232 <data name="param_svm_xval_out" format="tabular"/>
0
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233 </outputs>
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234 <help>Detects features in MS1 data based on peptide identifications.
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235
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236
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237 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FeatureFinderIdentification.html</help>
3a61c78033f0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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238 </tool>