annotate MSSimulator.xml @ 6:e8f47f874cae draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
author galaxyp
date Tue, 20 Mar 2018 15:09:58 -0400
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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: [Utilities]-->
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4 <tool id="MSSimulator" name="MSSimulator" version="2.3.0">
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5 <description>A highly configurable simulator for mass spectrometry experiments.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">MSSimulator</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>MSSimulator
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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 #if $param_out:
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20 -out $param_out
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21 #end if
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22 #if $param_out_pm:
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23 -out_pm $param_out_pm
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24 #end if
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25 #if $param_out_fm:
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26 -out_fm $param_out_fm
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27 #end if
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28 #if $param_out_cm:
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29 -out_cm $param_out_cm
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30 #end if
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31 #if $param_out_lcm:
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32 -out_lcm $param_out_lcm
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33 #end if
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34 #if $param_out_cntm:
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35 -out_cntm $param_out_cntm
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36 #end if
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37 #if $param_out_id:
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38 -out_id $param_out_id
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39 #end if
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40 #if $param_algorithm_MSSim_Digestion_enzyme:
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41 -algorithm:MSSim:Digestion:enzyme
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42 #if " " in str($param_algorithm_MSSim_Digestion_enzyme):
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43 "$param_algorithm_MSSim_Digestion_enzyme"
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44 #else
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45 $param_algorithm_MSSim_Digestion_enzyme
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46 #end if
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47 #end if
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48 #if $param_algorithm_MSSim_Digestion_model:
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49 -algorithm:MSSim:Digestion:model
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50 #if " " in str($param_algorithm_MSSim_Digestion_model):
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51 "$param_algorithm_MSSim_Digestion_model"
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52 #else
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53 $param_algorithm_MSSim_Digestion_model
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54 #end if
0
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55 #end if
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56 #if $param_algorithm_MSSim_Digestion_min_peptide_length:
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57 -algorithm:MSSim:Digestion:min_peptide_length $param_algorithm_MSSim_Digestion_min_peptide_length
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58 #end if
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59 #if $param_algorithm_MSSim_Digestion_model_trained_threshold:
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60 -algorithm:MSSim:Digestion:model_trained:threshold $param_algorithm_MSSim_Digestion_model_trained_threshold
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61 #end if
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62 #if $param_algorithm_MSSim_Digestion_model_naive_missed_cleavages:
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63 -algorithm:MSSim:Digestion:model_naive:missed_cleavages $param_algorithm_MSSim_Digestion_model_naive_missed_cleavages
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64 #end if
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65 #if $param_algorithm_MSSim_RT_rt_column:
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66 -algorithm:MSSim:RT:rt_column
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67 #if " " in str($param_algorithm_MSSim_RT_rt_column):
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68 "$param_algorithm_MSSim_RT_rt_column"
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69 #else
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70 $param_algorithm_MSSim_RT_rt_column
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71 #end if
0
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72 #end if
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73 #if $param_algorithm_MSSim_RT_auto_scale:
1
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74 -algorithm:MSSim:RT:auto_scale
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75 #if " " in str($param_algorithm_MSSim_RT_auto_scale):
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76 "$param_algorithm_MSSim_RT_auto_scale"
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77 #else
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78 $param_algorithm_MSSim_RT_auto_scale
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79 #end if
0
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80 #end if
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81 #if $param_algorithm_MSSim_RT_total_gradient_time:
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82 -algorithm:MSSim:RT:total_gradient_time $param_algorithm_MSSim_RT_total_gradient_time
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83 #end if
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84 #if $param_algorithm_MSSim_RT_sampling_rate:
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85 -algorithm:MSSim:RT:sampling_rate $param_algorithm_MSSim_RT_sampling_rate
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86 #end if
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87 #if $param_algorithm_MSSim_RT_scan_window_min:
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88 -algorithm:MSSim:RT:scan_window:min $param_algorithm_MSSim_RT_scan_window_min
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89 #end if
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90 #if $param_algorithm_MSSim_RT_scan_window_max:
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91 -algorithm:MSSim:RT:scan_window:max $param_algorithm_MSSim_RT_scan_window_max
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92 #end if
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93 #if $param_algorithm_MSSim_RT_variation_feature_stddev:
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94 -algorithm:MSSim:RT:variation:feature_stddev $param_algorithm_MSSim_RT_variation_feature_stddev
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95 #end if
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96 #if $param_algorithm_MSSim_RT_variation_affine_offset:
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97 -algorithm:MSSim:RT:variation:affine_offset $param_algorithm_MSSim_RT_variation_affine_offset
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98 #end if
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99 #if $param_algorithm_MSSim_RT_variation_affine_scale:
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100 -algorithm:MSSim:RT:variation:affine_scale $param_algorithm_MSSim_RT_variation_affine_scale
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101 #end if
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102 #if $param_algorithm_MSSim_RT_column_condition_distortion:
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103 -algorithm:MSSim:RT:column_condition:distortion $param_algorithm_MSSim_RT_column_condition_distortion
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104 #end if
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105 #if $param_algorithm_MSSim_RT_profile_shape_width_value:
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106 -algorithm:MSSim:RT:profile_shape:width:value $param_algorithm_MSSim_RT_profile_shape_width_value
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107 #end if
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108 #if $param_algorithm_MSSim_RT_profile_shape_width_variance:
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109 -algorithm:MSSim:RT:profile_shape:width:variance $param_algorithm_MSSim_RT_profile_shape_width_variance
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110 #end if
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111 #if $param_algorithm_MSSim_RT_profile_shape_skewness_value:
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112 -algorithm:MSSim:RT:profile_shape:skewness:value $param_algorithm_MSSim_RT_profile_shape_skewness_value
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113 #end if
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114 #if $param_algorithm_MSSim_RT_profile_shape_skewness_variance:
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115 -algorithm:MSSim:RT:profile_shape:skewness:variance $param_algorithm_MSSim_RT_profile_shape_skewness_variance
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116 #end if
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117 #if $param_algorithm_MSSim_RT_HPLC_model_file:
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118 -algorithm:MSSim:RT:HPLC:model_file "$param_algorithm_MSSim_RT_HPLC_model_file"
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119 #end if
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120 #if $param_algorithm_MSSim_RT_CE_pH:
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121 -algorithm:MSSim:RT:CE:pH $param_algorithm_MSSim_RT_CE_pH
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122 #end if
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123 #if $param_algorithm_MSSim_RT_CE_alpha:
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124 -algorithm:MSSim:RT:CE:alpha $param_algorithm_MSSim_RT_CE_alpha
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125 #end if
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126 #if $param_algorithm_MSSim_RT_CE_mu_eo:
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127 -algorithm:MSSim:RT:CE:mu_eo $param_algorithm_MSSim_RT_CE_mu_eo
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128 #end if
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129 #if $param_algorithm_MSSim_RT_CE_lenght_d:
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130 -algorithm:MSSim:RT:CE:lenght_d $param_algorithm_MSSim_RT_CE_lenght_d
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131 #end if
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132 #if $param_algorithm_MSSim_RT_CE_length_total:
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133 -algorithm:MSSim:RT:CE:length_total $param_algorithm_MSSim_RT_CE_length_total
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134 #end if
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135 #if $param_algorithm_MSSim_RT_CE_voltage:
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136 -algorithm:MSSim:RT:CE:voltage $param_algorithm_MSSim_RT_CE_voltage
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137 #end if
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138 #if $param_algorithm_MSSim_Detectability_dt_simulation_on:
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139 -algorithm:MSSim:Detectability:dt_simulation_on
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140 #end if
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141 #if $param_algorithm_MSSim_Detectability_min_detect:
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142 -algorithm:MSSim:Detectability:min_detect $param_algorithm_MSSim_Detectability_min_detect
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143 #end if
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144 #if $param_algorithm_MSSim_Detectability_dt_model_file:
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145 -algorithm:MSSim:Detectability:dt_model_file "$param_algorithm_MSSim_Detectability_dt_model_file"
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146 #end if
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147
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148 #if $rep_param_algorithm_MSSim_Ionization_esi_ionized_residues:
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149 -algorithm:MSSim:Ionization:esi:ionized_residues
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150 #for token in $rep_param_algorithm_MSSim_Ionization_esi_ionized_residues:
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151 #if " " in str(token):
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152 "$token.param_algorithm_MSSim_Ionization_esi_ionized_residues"
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153 #else
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154 $token.param_algorithm_MSSim_Ionization_esi_ionized_residues
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155 #end if
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156 #end for
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157 #end if
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158
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159 #if $rep_param_algorithm_MSSim_Ionization_esi_charge_impurity:
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160 -algorithm:MSSim:Ionization:esi:charge_impurity
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161 #for token in $rep_param_algorithm_MSSim_Ionization_esi_charge_impurity:
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162 #if " " in str(token):
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163 "$token.param_algorithm_MSSim_Ionization_esi_charge_impurity"
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164 #else
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165 $token.param_algorithm_MSSim_Ionization_esi_charge_impurity
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166 #end if
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167 #end for
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168 #end if
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169 #if $param_algorithm_MSSim_Ionization_esi_ionization_probability:
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170 -algorithm:MSSim:Ionization:esi:ionization_probability $param_algorithm_MSSim_Ionization_esi_ionization_probability
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171 #end if
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172
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173 #if $rep_param_algorithm_MSSim_Ionization_maldi_ionization_probabilities:
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174 -algorithm:MSSim:Ionization:maldi:ionization_probabilities
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175 #for token in $rep_param_algorithm_MSSim_Ionization_maldi_ionization_probabilities:
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176 #if " " in str(token):
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177 "$token.param_algorithm_MSSim_Ionization_maldi_ionization_probabilities"
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178 #else
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179 $token.param_algorithm_MSSim_Ionization_maldi_ionization_probabilities
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180 #end if
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181 #end for
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182 #end if
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183 #if $param_algorithm_MSSim_Ionization_mz_lower_measurement_limit:
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184 -algorithm:MSSim:Ionization:mz:lower_measurement_limit $param_algorithm_MSSim_Ionization_mz_lower_measurement_limit
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185 #end if
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186 #if $param_algorithm_MSSim_Ionization_mz_upper_measurement_limit:
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187 -algorithm:MSSim:Ionization:mz:upper_measurement_limit $param_algorithm_MSSim_Ionization_mz_upper_measurement_limit
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188 #end if
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189 #if $param_algorithm_MSSim_RawSignal_enabled:
1
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190 -algorithm:MSSim:RawSignal:enabled
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191 #if " " in str($param_algorithm_MSSim_RawSignal_enabled):
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192 "$param_algorithm_MSSim_RawSignal_enabled"
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193 #else
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194 $param_algorithm_MSSim_RawSignal_enabled
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195 #end if
0
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196 #end if
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197 #if $param_algorithm_MSSim_RawSignal_peak_shape:
1
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198 -algorithm:MSSim:RawSignal:peak_shape
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199 #if " " in str($param_algorithm_MSSim_RawSignal_peak_shape):
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200 "$param_algorithm_MSSim_RawSignal_peak_shape"
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201 #else
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202 $param_algorithm_MSSim_RawSignal_peak_shape
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203 #end if
0
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204 #end if
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205 #if $param_algorithm_MSSim_RawSignal_resolution_value:
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206 -algorithm:MSSim:RawSignal:resolution:value $param_algorithm_MSSim_RawSignal_resolution_value
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207 #end if
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208 #if $param_algorithm_MSSim_RawSignal_resolution_type:
1
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209 -algorithm:MSSim:RawSignal:resolution:type
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210 #if " " in str($param_algorithm_MSSim_RawSignal_resolution_type):
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211 "$param_algorithm_MSSim_RawSignal_resolution_type"
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212 #else
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213 $param_algorithm_MSSim_RawSignal_resolution_type
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214 #end if
0
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215 #end if
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216 #if $param_algorithm_MSSim_RawSignal_baseline_scaling:
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217 -algorithm:MSSim:RawSignal:baseline:scaling $param_algorithm_MSSim_RawSignal_baseline_scaling
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218 #end if
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219 #if $param_algorithm_MSSim_RawSignal_baseline_shape:
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220 -algorithm:MSSim:RawSignal:baseline:shape $param_algorithm_MSSim_RawSignal_baseline_shape
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221 #end if
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222 #if $param_algorithm_MSSim_RawSignal_mz_sampling_points:
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223 -algorithm:MSSim:RawSignal:mz:sampling_points $param_algorithm_MSSim_RawSignal_mz_sampling_points
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224 #end if
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225 #if $param_algorithm_MSSim_RawSignal_contaminants_file:
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226 -algorithm:MSSim:RawSignal:contaminants:file "$param_algorithm_MSSim_RawSignal_contaminants_file"
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227 #end if
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228 #if $param_algorithm_MSSim_RawSignal_variation_mz_error_stddev:
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229 -algorithm:MSSim:RawSignal:variation:mz:error_stddev $param_algorithm_MSSim_RawSignal_variation_mz_error_stddev
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230 #end if
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231 #if $param_algorithm_MSSim_RawSignal_variation_mz_error_mean:
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232 -algorithm:MSSim:RawSignal:variation:mz:error_mean $param_algorithm_MSSim_RawSignal_variation_mz_error_mean
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233 #end if
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234 #if $param_algorithm_MSSim_RawSignal_variation_intensity_scale:
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235 -algorithm:MSSim:RawSignal:variation:intensity:scale $param_algorithm_MSSim_RawSignal_variation_intensity_scale
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236 #end if
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237 #if $param_algorithm_MSSim_RawSignal_variation_intensity_scale_stddev:
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238 -algorithm:MSSim:RawSignal:variation:intensity:scale_stddev $param_algorithm_MSSim_RawSignal_variation_intensity_scale_stddev
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239 #end if
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240 #if $param_algorithm_MSSim_RawSignal_noise_shot_rate:
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241 -algorithm:MSSim:RawSignal:noise:shot:rate $param_algorithm_MSSim_RawSignal_noise_shot_rate
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242 #end if
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243 #if $param_algorithm_MSSim_RawSignal_noise_shot_intensity_mean:
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244 -algorithm:MSSim:RawSignal:noise:shot:intensity-mean $param_algorithm_MSSim_RawSignal_noise_shot_intensity_mean
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245 #end if
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246 #if $param_algorithm_MSSim_RawSignal_noise_white_mean:
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247 -algorithm:MSSim:RawSignal:noise:white:mean $param_algorithm_MSSim_RawSignal_noise_white_mean
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248 #end if
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249 #if $param_algorithm_MSSim_RawSignal_noise_white_stddev:
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250 -algorithm:MSSim:RawSignal:noise:white:stddev $param_algorithm_MSSim_RawSignal_noise_white_stddev
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251 #end if
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252 #if $param_algorithm_MSSim_RawSignal_noise_detector_mean:
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253 -algorithm:MSSim:RawSignal:noise:detector:mean $param_algorithm_MSSim_RawSignal_noise_detector_mean
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254 #end if
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255 #if $param_algorithm_MSSim_RawSignal_noise_detector_stddev:
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256 -algorithm:MSSim:RawSignal:noise:detector:stddev $param_algorithm_MSSim_RawSignal_noise_detector_stddev
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257 #end if
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258 #if $param_algorithm_MSSim_RawTandemSignal_status:
1
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259 -algorithm:MSSim:RawTandemSignal:status
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260 #if " " in str($param_algorithm_MSSim_RawTandemSignal_status):
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261 "$param_algorithm_MSSim_RawTandemSignal_status"
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262 #else
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263 $param_algorithm_MSSim_RawTandemSignal_status
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264 #end if
0
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265 #end if
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266 #if $param_algorithm_MSSim_RawTandemSignal_tandem_mode:
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267 -algorithm:MSSim:RawTandemSignal:tandem_mode $param_algorithm_MSSim_RawTandemSignal_tandem_mode
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268 #end if
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269 #if $param_algorithm_MSSim_RawTandemSignal_svm_model_set_file:
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270 -algorithm:MSSim:RawTandemSignal:svm_model_set_file "$param_algorithm_MSSim_RawTandemSignal_svm_model_set_file"
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271 #end if
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272 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ms2_spectra_per_rt_bin:
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273 -algorithm:MSSim:RawTandemSignal:Precursor:ms2_spectra_per_rt_bin $param_algorithm_MSSim_RawTandemSignal_Precursor_ms2_spectra_per_rt_bin
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274 #end if
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275 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_min_mz_peak_distance:
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276 -algorithm:MSSim:RawTandemSignal:Precursor:min_mz_peak_distance $param_algorithm_MSSim_RawTandemSignal_Precursor_min_mz_peak_distance
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277 #end if
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278 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_mz_isolation_window:
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279 -algorithm:MSSim:RawTandemSignal:Precursor:mz_isolation_window $param_algorithm_MSSim_RawTandemSignal_Precursor_mz_isolation_window
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280 #end if
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281 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_exclude_overlapping_peaks:
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282 -algorithm:MSSim:RawTandemSignal:Precursor:exclude_overlapping_peaks
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283 #end if
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284
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285 #if $rep_param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter:
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286 -algorithm:MSSim:RawTandemSignal:Precursor:charge_filter
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287 #for token in $rep_param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter:
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288 #if " " in str(token):
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289 "$token.param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter"
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290 #else
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291 $token.param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter
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292 #end if
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293 #end for
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294 #end if
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295 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_use_dynamic_exclusion:
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296 -algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:use_dynamic_exclusion
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297 #end if
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298 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_exclusion_time:
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299 -algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:exclusion_time $param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_exclusion_time
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300 #end if
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301 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_max_list_size:
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302 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:max_list_size $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_max_list_size
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303 #end if
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304 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_min_rt:
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305 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:min_rt $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_min_rt
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306 #end if
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307 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_max_rt:
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308 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:max_rt $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_max_rt
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309 #end if
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310 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_step_size:
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311 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_step_size $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_step_size
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312 #end if
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313 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_window_size:
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314 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_window_size $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_window_size
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315 #end if
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316 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_protein_id_probability:
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317 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_protein_id_probability $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_protein_id_probability
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318 #end if
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319 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_pt_weight:
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320 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_pt_weight $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_pt_weight
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321 #end if
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322 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_mz:
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323 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_mz $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_mz
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324 #end if
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325 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_max_mz:
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326 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:max_mz $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_max_mz
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327 #end if
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328 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_use_peptide_rule:
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329 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:use_peptide_rule
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330 #end if
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331 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_ids:
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332 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_ids $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_ids
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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333 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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334 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_probability:
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335 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_probability $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_probability
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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336 #end if
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337 #if $param_algorithm_MSSim_RawTandemSignal_MS_E_add_single_spectra:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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338 -algorithm:MSSim:RawTandemSignal:MS_E:add_single_spectra
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339 #end if
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340 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_isotopes:
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341 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_isotopes
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342 #end if
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343 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_max_isotope:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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344 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:max_isotope $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_max_isotope
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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345 #end if
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346 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_metainfo:
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347 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_metainfo
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348 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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349 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_losses:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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350 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses
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351 #end if
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352 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_precursor_peaks:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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353 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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354 #end if
1
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355 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_all_precursor_charges:
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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356 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_all_precursor_charges
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
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357 #end if
0
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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358 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_abundant_immonium_ions:
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359 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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360 #end if
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361 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_first_prefix_ion:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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362 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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363 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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364 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions:
1
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
365 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_y_ions
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
366 #if " " in str($param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions):
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
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diff changeset
367 "$param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions"
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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diff changeset
368 #else
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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369 $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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parents: 0
diff changeset
370 #end if
0
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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371 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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372 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions:
1
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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parents: 0
diff changeset
373 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_b_ions
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
374 #if " " in str($param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions):
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
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diff changeset
375 "$param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions"
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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diff changeset
376 #else
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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377 $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
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diff changeset
378 #end if
0
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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379 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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380 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_a_ions:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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381 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_a_ions
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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382 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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383 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_c_ions:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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384 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_c_ions
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diff changeset
385 #end if
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386 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_x_ions:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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387 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_x_ions
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
388 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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389 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_z_ions:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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390 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_z_ions
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
391 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
392 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_y_intensity:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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393 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:y_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_y_intensity
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
394 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
395 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_b_intensity:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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396 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:b_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_b_intensity
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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397 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
398 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_a_intensity:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
399 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:a_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_a_intensity
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
400 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
401 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_c_intensity:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
402 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:c_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_c_intensity
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff changeset
403 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
404 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_x_intensity:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
405 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:x_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_x_intensity
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
406 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
407 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_z_intensity:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
408 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:z_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_z_intensity
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
409 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
410 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_relative_loss_intensity:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
411 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:relative_loss_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_relative_loss_intensity
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
412 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
413 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_intensity:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
414 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_intensity
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
415 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
416 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_H2O_intensity:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
417 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_H2O_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_H2O_intensity
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
418 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
419 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_NH3_intensity:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
420 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_NH3_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_NH3_intensity
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
421 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
422 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_isotopes:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
423 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_isotopes
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
424 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
425 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_max_isotope:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
426 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:max_isotope $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_max_isotope
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
427 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
428 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_metainfo:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
429 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_metainfo
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
430 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
431 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_first_prefix_ion:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
432 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_first_prefix_ion
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
433 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
434 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_y_ions:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
435 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y_ions
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
436 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
437 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_y2_ions:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
438 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y2_ions
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
439 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
440 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_b_ions:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
441 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b_ions
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
442 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
443 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_b2_ions:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
444 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b2_ions
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
445 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
446 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_a_ions:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
447 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_a_ions
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
448 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
449 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_c_ions:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
450 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_c_ions
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
451 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
452 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_x_ions:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
453 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_x_ions
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
454 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
455 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_z_ions:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
456 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_z_ions
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
457 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
458 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_losses:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
459 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_losses
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
460 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
461 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_y_intensity:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
462 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:y_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_y_intensity
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
463 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
464 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_b_intensity:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
465 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:b_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_b_intensity
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
466 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
467 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_a_intensity:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
468 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:a_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_a_intensity
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
469 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
470 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_c_intensity:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
471 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:c_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_c_intensity
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
472 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
473 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_x_intensity:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
474 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:x_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_x_intensity
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
475 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
476 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_z_intensity:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
477 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:z_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_z_intensity
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
478 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
479 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_relative_loss_intensity:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
480 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:relative_loss_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_relative_loss_intensity
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
481 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
482 #if $param_algorithm_MSSim_Global_ionization_type:
1
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
483 -algorithm:MSSim:Global:ionization_type
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
484 #if " " in str($param_algorithm_MSSim_Global_ionization_type):
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
485 "$param_algorithm_MSSim_Global_ionization_type"
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
486 #else
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
487 $param_algorithm_MSSim_Global_ionization_type
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
488 #end if
0
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
489 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
490 #if $param_algorithm_MSSim_Labeling_type:
1
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
491 -algorithm:MSSim:Labeling:type
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
492 #if " " in str($param_algorithm_MSSim_Labeling_type):
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
493 "$param_algorithm_MSSim_Labeling_type"
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
494 #else
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
495 $param_algorithm_MSSim_Labeling_type
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
496 #end if
0
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
497 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
498 #if $param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
499 -algorithm:MSSim:Labeling:ICPL:ICPL_fixed_rtshift $param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
500 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
501 #if $param_algorithm_MSSim_Labeling_ICPL_label_proteins:
1
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
502 -algorithm:MSSim:Labeling:ICPL:label_proteins
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
503 #if " " in str($param_algorithm_MSSim_Labeling_ICPL_label_proteins):
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
504 "$param_algorithm_MSSim_Labeling_ICPL_label_proteins"
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
505 #else
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
506 $param_algorithm_MSSim_Labeling_ICPL_label_proteins
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
507 #end if
0
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
508 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
509 #if $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
510 -algorithm:MSSim:Labeling:SILAC:fixed_rtshift $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
511 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
512 #if $param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_lysine:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
513 -algorithm:MSSim:Labeling:SILAC:medium_channel:modification_lysine "$param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_lysine"
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
514 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
515 #if $param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_arginine:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
516 -algorithm:MSSim:Labeling:SILAC:medium_channel:modification_arginine "$param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_arginine"
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
517 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
518 #if $param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_lysine:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
519 -algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_lysine "$param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_lysine"
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
520 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
521 #if $param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
522 -algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_arginine "$param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine"
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
523 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
524 #if $param_algorithm_MSSim_Labeling_itraq_iTRAQ:
1
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
525 -algorithm:MSSim:Labeling:itraq:iTRAQ
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
526 #if " " in str($param_algorithm_MSSim_Labeling_itraq_iTRAQ):
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
527 "$param_algorithm_MSSim_Labeling_itraq_iTRAQ"
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
528 #else
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
529 $param_algorithm_MSSim_Labeling_itraq_iTRAQ
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
530 #end if
0
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
531 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
532 #if $param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
533 -algorithm:MSSim:Labeling:itraq:reporter_mass_shift $param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
534 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
535
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
536 #if $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_4plex:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
537 -algorithm:MSSim:Labeling:itraq:channel_active_4plex
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
538 #for token in $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_4plex:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
539 #if " " in str(token):
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
540 "$token.param_algorithm_MSSim_Labeling_itraq_channel_active_4plex"
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
541 #else
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
542 $token.param_algorithm_MSSim_Labeling_itraq_channel_active_4plex
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
543 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
544 #end for
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
545 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
546
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
547 #if $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_8plex:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
548 -algorithm:MSSim:Labeling:itraq:channel_active_8plex
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
549 #for token in $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_8plex:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
550 #if " " in str(token):
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
551 "$token.param_algorithm_MSSim_Labeling_itraq_channel_active_8plex"
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
552 #else
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
553 $token.param_algorithm_MSSim_Labeling_itraq_channel_active_8plex
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
554 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
555 #end for
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
556 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
557 #if $param_algorithm_MSSim_Labeling_itraq_Y_contamination:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
558 -algorithm:MSSim:Labeling:itraq:Y_contamination $param_algorithm_MSSim_Labeling_itraq_Y_contamination
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
559 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
560 #if $param_algorithm_MSSim_Labeling_o18_labeling_efficiency:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
561 -algorithm:MSSim:Labeling:o18:labeling_efficiency $param_algorithm_MSSim_Labeling_o18_labeling_efficiency
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
562 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
563 #if $param_algorithm_RandomNumberGenerators_biological:
1
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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parents: 0
diff changeset
564 -algorithm:RandomNumberGenerators:biological
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
565 #if " " in str($param_algorithm_RandomNumberGenerators_biological):
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
566 "$param_algorithm_RandomNumberGenerators_biological"
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
567 #else
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
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parents: 0
diff changeset
568 $param_algorithm_RandomNumberGenerators_biological
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
569 #end if
0
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
570 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
571 #if $param_algorithm_RandomNumberGenerators_technical:
1
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
572 -algorithm:RandomNumberGenerators:technical
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
573 #if " " in str($param_algorithm_RandomNumberGenerators_technical):
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
574 "$param_algorithm_RandomNumberGenerators_technical"
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
575 #else
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
576 $param_algorithm_RandomNumberGenerators_technical
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
577 #end if
0
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
578 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
579 #if $adv_opts.adv_opts_selector=='advanced':
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
580 #if $adv_opts.param_force:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
581 -force
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
582 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
583 #if $adv_opts.param_algorithm_MSSim_Ionization_esi_max_impurity_set_size:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
584 -algorithm:MSSim:Ionization:esi:max_impurity_set_size $adv_opts.param_algorithm_MSSim_Ionization_esi_max_impurity_set_size
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
585 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
586 #if $adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_light_channel_label:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
587 -algorithm:MSSim:Labeling:ICPL:ICPL_light_channel_label "$adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_light_channel_label"
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
588 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
589 #if $adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_medium_channel_label:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
590 -algorithm:MSSim:Labeling:ICPL:ICPL_medium_channel_label "$adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_medium_channel_label"
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
591 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
592 #if $adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_heavy_channel_label:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
593 -algorithm:MSSim:Labeling:ICPL:ICPL_heavy_channel_label "$adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_heavy_channel_label"
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
594 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
595
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
596 #if $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
597 -algorithm:MSSim:Labeling:itraq:isotope_correction_values_4plex
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
598 #for token in $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
599 #if " " in str(token):
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
600 "$token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex"
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
601 #else
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
602 $token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
603 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
604 #end for
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
605 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
606
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
607 #if $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
608 -algorithm:MSSim:Labeling:itraq:isotope_correction_values_8plex
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
609 #for token in $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex:
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
610 #if " " in str(token):
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
611 "$token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex"
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
612 #else
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
613 $token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
614 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
615 #end for
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
616 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
617 #end if
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
618 </command>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
619 <inputs>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
620 <param name="param_in" type="data" format="fasta" multiple="true" optional="False" size="30" label="Input protein sequences" help="(-in) ">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
621 <sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
622 <valid initial="string.printable">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
623 <remove value="'"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
624 <remove value="&quot;"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
625 </valid>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
626 </sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
627 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
628 <param name="param_algorithm_MSSim_Digestion_enzyme" type="select" optional="False" value="Trypsin" label="Enzyme to use for digestion (select 'no cleavage' to skip digestion)" help="(-enzyme) ">
5
66f0ddeb23f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents: 1
diff changeset
629 <option value="CNBr">CNBr</option>
1
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
630 <option value="Trypsin/P">Trypsin/P</option>
5
66f0ddeb23f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents: 1
diff changeset
631 <option value="Lys-C">Lys-C</option>
1
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
632 <option value="Formic_acid">Formic_acid</option>
5
66f0ddeb23f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents: 1
diff changeset
633 <option value="Arg-C/P">Arg-C/P</option>
66f0ddeb23f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents: 1
diff changeset
634 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
66f0ddeb23f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents: 1
diff changeset
635 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
66f0ddeb23f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents: 1
diff changeset
636 <option value="proline endopeptidase">proline endopeptidase</option>
66f0ddeb23f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents: 1
diff changeset
637 <option value="Arg-C">Arg-C</option>
66f0ddeb23f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents: 1
diff changeset
638 <option value="unspecific cleavage">unspecific cleavage</option>
66f0ddeb23f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents: 1
diff changeset
639 <option value="Trypsin" selected="true">Trypsin</option>
1
a4c3db6825f4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
galaxyp
parents: 0
diff changeset
640 <option value="TrypChymo">TrypChymo</option>
5
66f0ddeb23f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents: 1
diff changeset
641 <option value="V8-E">V8-E</option>
66f0ddeb23f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents: 1
diff changeset
642 <option value="2-iodobenzoate">2-iodobenzoate</option>
66f0ddeb23f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents: 1
diff changeset
643 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
66f0ddeb23f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents: 1
diff changeset
644 <option value="no cleavage">no cleavage</option>
66f0ddeb23f3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
galaxyp
parents: 1
diff changeset
645 <option value="Asp-N_ambic">Asp-N_ambic</option>
1
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parents: 0
diff changeset
646 <option value="PepsinA">PepsinA</option>
5
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parents: 1
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647 <option value="Chymotrypsin">Chymotrypsin</option>
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parents: 1
diff changeset
648 <option value="V8-DE">V8-DE</option>
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parents: 1
diff changeset
649 <option value="Asp-N/B">Asp-N/B</option>
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parents: 1
diff changeset
650 <option value="Lys-N">Lys-N</option>
1
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parents: 0
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651 <option value="Lys-C/P">Lys-C/P</option>
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parents: 0
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652 <option value="leukocyte elastase">leukocyte elastase</option>
5
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parents: 1
diff changeset
653 <option value="Asp-N">Asp-N</option>
0
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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654 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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655 <param name="param_algorithm_MSSim_Digestion_model" display="radio" type="select" optional="False" value="naive" label="The cleavage model to use for digestion" help="(-model) 'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u)">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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656 <option value="trained">trained</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff changeset
657 <option value="naive" selected="true">naive</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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658 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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659 <param name="param_algorithm_MSSim_Digestion_min_peptide_length" type="integer" min="1" optional="True" value="3" label="Minimum peptide length after digestion (shorter ones will be discarded)" help="(-min_peptide_length) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
660 <param name="param_algorithm_MSSim_Digestion_model_trained_threshold" type="float" min="-2.0" max="4.0" optional="True" value="0.5" label="Model threshold for calling a cleavage" help="(-threshold) Higher values increase the number of cleavages. -2 will give no cleavages, +4 almost full cleavage"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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661 <param name="param_algorithm_MSSim_Digestion_model_naive_missed_cleavages" type="integer" min="0" optional="True" value="1" label="Maximum number of missed cleavages considered" help="(-missed_cleavages) All possible resulting peptides will be created"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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662 <param name="param_algorithm_MSSim_RT_rt_column" display="radio" type="select" optional="False" value="HPLC" label="Modelling of an RT or CE column" help="(-rt_column) ">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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663 <option value="none">none</option>
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664 <option value="HPLC" selected="true">HPLC</option>
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665 <option value="CE">CE</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
666 </param>
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667 <param name="param_algorithm_MSSim_RT_auto_scale" display="radio" type="select" optional="False" value="true" label="Scale predicted RT's/MT's to given 'total_gradient_time'?" help="(-auto_scale) If 'true', for CE this means that 'CE:lenght_d', 'CE:length_total', 'CE:voltage' have no influence">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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668 <option value="true" selected="true">true</option>
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diff changeset
669 <option value="false">false</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
670 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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671 <param name="param_algorithm_MSSim_RT_total_gradient_time" type="float" min="1e-05" optional="True" value="2500.0" label="The duration [s] of the gradient" help="(-total_gradient_time) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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672 <param name="param_algorithm_MSSim_RT_sampling_rate" type="float" min="0.01" max="60.0" optional="True" value="2.0" label="Time interval [s] between consecutive scans" help="(-sampling_rate) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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673 <param name="param_algorithm_MSSim_RT_scan_window_min" type="float" min="0.0" optional="True" value="500.0" label="Start of RT Scan Window [s]" help="(-min) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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674 <param name="param_algorithm_MSSim_RT_scan_window_max" type="float" min="1.0" optional="True" value="1500.0" label="End of RT Scan Window [s]" help="(-max) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
675 <param name="param_algorithm_MSSim_RT_variation_feature_stddev" type="integer" value="3" label="Standard deviation of shift in retention time [s] from predicted model (applied to every single feature independently)" help="(-feature_stddev) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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676 <param name="param_algorithm_MSSim_RT_variation_affine_offset" type="integer" value="0" label="Global offset in retention time [s] from predicted model" help="(-affine_offset) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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677 <param name="param_algorithm_MSSim_RT_variation_affine_scale" type="integer" value="1" label="Global scaling in retention time from predicted model" help="(-affine_scale) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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678 <param name="param_algorithm_MSSim_RT_column_condition_distortion" type="integer" min="0" max="10" optional="True" value="0" label="Distortion of the elution profiles. Good presets are 0 for a perfect elution profile, 1 for a slightly distorted elution profile etc... For trapping instruments (" help="(-distortion) e.g. Orbitrap) distortion should be &gt;4"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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679 <param name="param_algorithm_MSSim_RT_profile_shape_width_value" type="float" min="0.0" optional="True" value="9.0" label="Width of the Exponential Gaussian Hybrid distribution shape of the elution profile" help="(-value) This does not correspond directly to the width in [s]"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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680 <param name="param_algorithm_MSSim_RT_profile_shape_width_variance" type="float" min="0.0" optional="True" value="1.6" label="Random component of the width (set to 0 to disable randomness), i.e" help="(-variance) scale parameter for the lorentzian variation of the variance (Note: The scale parameter has to be &gt;= 0)"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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681 <param name="param_algorithm_MSSim_RT_profile_shape_skewness_value" type="float" value="0.1" label="Asymmetric component of the EGH" help="(-value) Higher absolute(!) values lead to more skewness (negative values cause fronting, positive values cause tailing). Tau parameter of the EGH, i.e. time constant of the exponential decay of the Exponential Gaussian Hybrid distribution shape of the elution profile"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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682 <param name="param_algorithm_MSSim_RT_profile_shape_skewness_variance" type="float" min="0.0" optional="True" value="0.3" label="Random component of skewness (set to 0 to disable randomness), i.e" help="(-variance) scale parameter for the lorentzian variation of the time constant (Note: The scale parameter has to be &gt; 0)"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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683 <param name="param_algorithm_MSSim_RT_HPLC_model_file" type="text" size="30" value="examples/simulation/RTPredict.model" label="SVM model for retention time prediction" help="(-model_file) ">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
684 <sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
685 <valid initial="string.printable">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
686 <remove value="'"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
687 <remove value="&quot;"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
688 </valid>
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diff changeset
689 </sanitizer>
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diff changeset
690 </param>
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691 <param name="param_algorithm_MSSim_RT_CE_pH" type="float" min="0.0" max="14.0" optional="True" value="3.0" label="pH of buffe" help="(-pH) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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692 <param name="param_algorithm_MSSim_RT_CE_alpha" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Exponent Alpha used to calculate mobility" help="(-alpha) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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693 <param name="param_algorithm_MSSim_RT_CE_mu_eo" type="float" min="0.0" max="5.0" optional="True" value="0.0" label="Electroosmotic flow" help="(-mu_eo) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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694 <param name="param_algorithm_MSSim_RT_CE_lenght_d" type="float" min="0.0" max="1000.0" optional="True" value="70.0" label="Length of capillary [cm] from injection site to MS" help="(-lenght_d) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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695 <param name="param_algorithm_MSSim_RT_CE_length_total" type="float" min="0.0" max="1000.0" optional="True" value="75.0" label="Total length of capillary [cm]" help="(-length_total) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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696 <param name="param_algorithm_MSSim_RT_CE_voltage" type="float" min="0.0" optional="True" value="1000.0" label="Voltage applied to capillary" help="(-voltage) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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697 <param name="param_algorithm_MSSim_Detectability_dt_simulation_on" display="radio" type="boolean" truevalue="-algorithm:MSSim:Detectability:dt_simulation_on" falsevalue="" checked="false" optional="True" label="Modelling detectibility enabled?" help="(-dt_simulation_on) This can serve as a filter to remove peptides which ionize badly, thus reducing peptide count"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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698 <param name="param_algorithm_MSSim_Detectability_min_detect" type="float" value="0.5" label="Minimum peptide detectability accepted" help="(-min_detect) Peptides with a lower score will be removed"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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699 <param name="param_algorithm_MSSim_Detectability_dt_model_file" type="text" size="30" value="examples/simulation/DTPredict.model" label="SVM model for peptide detectability prediction" help="(-dt_model_file) ">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
700 <sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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701 <valid initial="string.printable">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
702 <remove value="'"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
703 <remove value="&quot;"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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704 </valid>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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705 </sanitizer>
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706 </param>
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707 <repeat name="rep_param_algorithm_MSSim_Ionization_esi_ionized_residues" min="0" max="1" title="param_algorithm_MSSim_Ionization_esi_ionized_residues">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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708 <param name="param_algorithm_MSSim_Ionization_esi_ionized_residues" type="select" optional="True" value="Arg Lys His" label="List of residues (as three letter code) that will be considered during ES ionization" help="(-ionized_residues) The N-term is always assumed to carry a charge. This parameter will be ignored during MALDI ionization">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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709 <option value="Ala">Ala</option>
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710 <option value="Cys">Cys</option>
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711 <option value="Asp">Asp</option>
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712 <option value="Glu">Glu</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
713 <option value="Phe">Phe</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
714 <option value="Gly">Gly</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
715 <option value="His">His</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
716 <option value="Ile">Ile</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
717 <option value="Lys">Lys</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
718 <option value="Leu">Leu</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
719 <option value="Met">Met</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
720 <option value="Asn">Asn</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
721 <option value="Pro">Pro</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
722 <option value="Gln">Gln</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
723 <option value="Arg">Arg</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
724 <option value="Sec">Sec</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
725 <option value="Ser">Ser</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
726 <option value="Thr">Thr</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
727 <option value="Val">Val</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
728 <option value="Trp">Trp</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
729 <option value="Tyr">Tyr</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
730 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
731 </repeat>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
732 <repeat name="rep_param_algorithm_MSSim_Ionization_esi_charge_impurity" min="0" max="1" title="param_algorithm_MSSim_Ionization_esi_charge_impurity">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
733 <param name="param_algorithm_MSSim_Ionization_esi_charge_impurity" type="text" size="30" value="H+:1" label="List of charged ions that contribute to charge with weight of occurrence (their sum is scaled to 1 internally)," help="(-charge_impurity) e.g. ['H:1'] or ['H:0.7' 'Na:0.3'], ['H:4' 'Na:1'] (which internally translates to ['H:0.8' 'Na:0.2'])">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
734 <sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
735 <valid initial="string.printable">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
736 <remove value="'"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
737 <remove value="&quot;"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
738 </valid>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
739 </sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
740 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
741 </repeat>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
742 <param name="param_algorithm_MSSim_Ionization_esi_ionization_probability" type="float" value="0.8" label="Probability for the binomial distribution of the ESI charge states" help="(-ionization_probability) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
743 <repeat name="rep_param_algorithm_MSSim_Ionization_maldi_ionization_probabilities" min="0" max="1" title="param_algorithm_MSSim_Ionization_maldi_ionization_probabilities">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
744 <param name="param_algorithm_MSSim_Ionization_maldi_ionization_probabilities" type="text" size="30" value="0.9 0.1" label="List of probabilities for the different charge states during MALDI ionization (the list must sum up to 1.0)" help="(-ionization_probabilities) ">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
745 <sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
746 <valid initial="string.printable">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
747 <remove value="'"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
748 <remove value="&quot;"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
749 </valid>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
750 </sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
751 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
752 </repeat>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
753 <param name="param_algorithm_MSSim_Ionization_mz_lower_measurement_limit" type="float" min="0.0" optional="True" value="200.0" label="Lower m/z detector limit" help="(-lower_measurement_limit) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
754 <param name="param_algorithm_MSSim_Ionization_mz_upper_measurement_limit" type="float" min="0.0" optional="True" value="2500.0" label="Upper m/z detector limit" help="(-upper_measurement_limit) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
755 <param name="param_algorithm_MSSim_RawSignal_enabled" display="radio" type="select" optional="False" value="true" label="Enable RAW signal simulation?" help="(-enabled) (select 'false' if you only need feature-maps)">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
756 <option value="true" selected="true">true</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
757 <option value="false">false</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
758 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
759 <param name="param_algorithm_MSSim_RawSignal_peak_shape" display="radio" type="select" optional="False" value="Gaussian" label="Peak Shape used around each isotope peak (be aware that the area under the curve is constant for both types, but the maximal height will differ (~ 2:3 = Lorentz:Gaussian) due to the wider base of the Lorentzian" help="(-peak_shape) ">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
760 <option value="Gaussian" selected="true">Gaussian</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
761 <option value="Lorentzian">Lorentzian</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
762 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
763 <param name="param_algorithm_MSSim_RawSignal_resolution_value" type="integer" value="50000" label="Instrument resolution at 400 Th" help="(-value) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
764 <param name="param_algorithm_MSSim_RawSignal_resolution_type" display="radio" type="select" optional="False" value="linear" label="How does resolution change with increasing m/z?! QTOFs usually show 'constant' behavior, FTs have linear degradation, and on Orbitraps the resolution decreases with square root of mass" help="(-type) ">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
765 <option value="constant">constant</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
766 <option value="linear" selected="true">linear</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
767 <option value="sqrt">sqrt</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
768 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
769 <param name="param_algorithm_MSSim_RawSignal_baseline_scaling" type="float" min="0.0" optional="True" value="0.0" label="Scale of baseline" help="(-scaling) Set to 0 to disable simulation of baseline"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
770 <param name="param_algorithm_MSSim_RawSignal_baseline_shape" type="float" min="0.0" optional="True" value="0.5" label="The baseline is modeled by an exponential probability density function (pdf) with f(x) = shape*e^(- shape*x)" help="(-shape) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
771 <param name="param_algorithm_MSSim_RawSignal_mz_sampling_points" type="integer" min="2" optional="True" value="3" label="Number of raw data points per FWHM of the peak" help="(-sampling_points) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
772 <param name="param_algorithm_MSSim_RawSignal_contaminants_file" type="text" size="30" value="examples/simulation/contaminants.csv" label="Contaminants file with sum formula and absolute RT interval" help="(-file) See 'OpenMS/examples/simulation/contaminants.txt' for details">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
773 <sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
774 <valid initial="string.printable">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
775 <remove value="'"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
776 <remove value="&quot;"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
777 </valid>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
778 </sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
779 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
780 <param name="param_algorithm_MSSim_RawSignal_variation_mz_error_stddev" type="float" value="0.0" label="Standard deviation for m/z errors" help="(-error_stddev) Set to 0 to disable simulation of m/z errors"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
781 <param name="param_algorithm_MSSim_RawSignal_variation_mz_error_mean" type="float" value="0.0" label="Average systematic m/z error (Da)" help="(-error_mean) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
782 <param name="param_algorithm_MSSim_RawSignal_variation_intensity_scale" type="float" min="0.0" optional="True" value="100.0" label="Constant scale factor of the feature intensity" help="(-scale) Set to 1.0 to get the real intensity values provided in the FASTA file"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
783 <param name="param_algorithm_MSSim_RawSignal_variation_intensity_scale_stddev" type="float" min="0.0" optional="True" value="0.0" label="Standard deviation of peak intensity (relative to the scaled peak height)" help="(-scale_stddev) Set to 0 to get simple rescaled intensities"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
784 <param name="param_algorithm_MSSim_RawSignal_noise_shot_rate" type="float" min="0.0" optional="True" value="0.0" label="Poisson rate of shot noise per unit m/z" help="(-rate) Set this to 0 to disable simulation of shot noise"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
785 <param name="param_algorithm_MSSim_RawSignal_noise_shot_intensity_mean" type="float" value="1.0" label="Shot noise intensity mean (exponentially distributed with given mean)" help="(-intensity-mean) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
786 <param name="param_algorithm_MSSim_RawSignal_noise_white_mean" type="float" value="0.0" label="Mean value of white noise being added to each measured signal" help="(-mean) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
787 <param name="param_algorithm_MSSim_RawSignal_noise_white_stddev" type="float" value="0.0" label="Standard deviation of white noise being added to each measured signal" help="(-stddev) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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788 <param name="param_algorithm_MSSim_RawSignal_noise_detector_mean" type="float" value="0.0" label="Mean value of the detector noise being added to the complete measurement" help="(-mean) "/>
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789 <param name="param_algorithm_MSSim_RawSignal_noise_detector_stddev" type="float" value="0.0" label="Standard deviation of the detector noise being added to the complete measurement" help="(-stddev) "/>
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790 <param name="param_algorithm_MSSim_RawTandemSignal_status" display="radio" type="select" optional="False" value="disabled" label="Create Tandem-MS scans?" help="(-status) ">
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791 <option value="disabled" selected="true">disabled</option>
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792 <option value="precursor">precursor</option>
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793 <option value="MS^E">MS^E</option>
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794 </param>
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795 <param name="param_algorithm_MSSim_RawTandemSignal_tandem_mode" type="integer" min="0" max="2" optional="True" value="0" label="Algorithm to generate the tandem-MS spectra" help="(-tandem_mode) 0 - fixed intensities, 1 - SVC prediction (abundant/missing), 2 - SVR prediction of peak intensity &lt;br&gt;"/>
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796 <param name="param_algorithm_MSSim_RawTandemSignal_svm_model_set_file" type="text" size="30" value="examples/simulation/SvmModelSet.model" label="File containing the filenames of SVM Models for different charge variants" help="(-svm_model_set_file) ">
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797 <sanitizer>
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798 <valid initial="string.printable">
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799 <remove value="'"/>
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800 <remove value="&quot;"/>
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801 </valid>
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802 </sanitizer>
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803 </param>
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804 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ms2_spectra_per_rt_bin" type="integer" min="1" optional="True" value="5" label="Number of allowed MS/MS spectra in a retention time bin" help="(-ms2_spectra_per_rt_bin) "/>
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805 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_min_mz_peak_distance" type="float" min="0.0001" optional="True" value="2.0" label="The minimal distance (in Th) between two peaks for concurrent selection for fragmentation" help="(-min_mz_peak_distance) Also used to define the m/z width of an exclusion window (distance +/- from m/z of precursor). If you set this lower than the isotopic envelope of a peptide, you might get multiple fragment spectra pointing to the same precursor"/>
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806 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_mz_isolation_window" type="float" min="0.0" optional="True" value="2.0" label="All peaks within a mass window (in Th) of a selected peak are also selected for fragmentation" help="(-mz_isolation_window) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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807 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_exclude_overlapping_peaks" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:Precursor:exclude_overlapping_peaks" falsevalue="" checked="false" optional="True" label="If true, overlapping or nearby peaks (within 'min_mz_peak_distance') are excluded for selection" help="(-exclude_overlapping_peaks) "/>
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808 <repeat name="rep_param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter" min="0" max="1" title="param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter">
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809 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter" type="text" min="1" max="5" optional="True" size="30" value="2 3" label="Charges considered for MS2 fragmentation" help="(-charge_filter) ">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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810 <sanitizer>
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811 <valid initial="string.printable">
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812 <remove value="'"/>
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813 <remove value="&quot;"/>
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814 </valid>
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815 </sanitizer>
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816 </param>
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817 </repeat>
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818 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_use_dynamic_exclusion" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:use_dynamic_exclusion" falsevalue="" checked="false" optional="True" label="If true dynamic exclusion is applied" help="(-use_dynamic_exclusion) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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819 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_exclusion_time" type="float" min="0.0" optional="True" value="100.0" label="The time (in seconds) a feature is excluded" help="(-exclusion_time) "/>
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820 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_max_list_size" type="integer" min="1" optional="True" value="1000" label="The maximal number of precursors in the inclusion list" help="(-max_list_size) "/>
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821 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_min_rt" type="float" min="0.0" optional="True" value="960.0" label="Minimal rt in seconds" help="(-min_rt) "/>
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822 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_max_rt" type="float" min="0.0" optional="True" value="3840.0" label="Maximal rt in seconds" help="(-max_rt) "/>
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823 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_step_size" type="float" min="1.0" optional="True" value="30.0" label="rt step size in seconds" help="(-rt_step_size) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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824 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_window_size" type="integer" min="1" optional="True" value="100" label="rt window size in seconds" help="(-rt_window_size) "/>
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825 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_protein_id_probability" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="Minimal protein probability for a protein to be considered identified" help="(-min_protein_id_probability) "/>
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826 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_pt_weight" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal pt weight of a precurso" help="(-min_pt_weight) "/>
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827 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_mz" type="float" min="0.0" optional="True" value="500.0" label="Minimal mz to be considered in protein based LP formulation" help="(-min_mz) "/>
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828 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_max_mz" type="float" min="0.0" optional="True" value="5000.0" label="Minimal mz to be considered in protein based LP formulation" help="(-max_mz) "/>
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829 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_use_peptide_rule" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:use_peptide_rule" falsevalue="" checked="false" optional="True" label="Use peptide rule instead of minimal protein id probability" help="(-use_peptide_rule) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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830 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_ids" type="integer" min="1" optional="True" value="2" label="If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id" help="(-min_peptide_ids) "/>
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831 <param name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_probability" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified" help="(-min_peptide_probability) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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832 <param name="param_algorithm_MSSim_RawTandemSignal_MS_E_add_single_spectra" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:MS_E:add_single_spectra" falsevalue="" checked="false" optional="True" label="If true, the MS2 spectra for each peptide signal are included in the output (might be a lot)" help="(-add_single_spectra) They will have a meta value 'MSE_DebugSpectrum' attached, so they can be filtered out. Native MS_E spectra will have 'MSE_Spectrum' instead"/>
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833 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_isotopes" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_isotopes" falsevalue="" checked="false" optional="True" label="If set to 1 isotope peaks of the product ion peaks are added" help="(-add_isotopes) "/>
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834 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_max_isotope" type="integer" value="2" label="Defines the maximal isotopic peak which is added, add_isotopes must be set to 1" help="(-max_isotope) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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835 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_metainfo" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_metainfo" falsevalue="" checked="false" optional="True" label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" help="(-add_metainfo) "/>
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836 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_losses" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses" falsevalue="" checked="false" optional="True" label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" help="(-add_losses) "/>
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837 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_precursor_peaks" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks" falsevalue="" checked="false" optional="True" label="Adds peaks of the precursor to the spectrum, which happen to occur sometimes" help="(-add_precursor_peaks) "/>
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838 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_all_precursor_charges" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_all_precursor_charges" falsevalue="" checked="false" optional="True" label="Adds precursor peaks with all charges in the given range" help="(-add_all_precursor_charges) "/>
0
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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839 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_abundant_immonium_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions" falsevalue="" checked="false" optional="True" label="Add most abundant immonium ions" help="(-add_abundant_immonium_ions) "/>
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840 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_first_prefix_ion" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion" falsevalue="" checked="false" optional="True" label="If set to true e.g. b1 ions are added" help="(-add_first_prefix_ion) "/>
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841 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions" display="radio" type="select" optional="False" value="true" label="Add peaks of y-ions to the spectrum" help="(-add_y_ions) ">
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842 <option value="true" selected="true">true</option>
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843 <option value="false">false</option>
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844 </param>
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845 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions" display="radio" type="select" optional="False" value="true" label="Add peaks of b-ions to the spectrum" help="(-add_b_ions) ">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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846 <option value="true" selected="true">true</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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847 <option value="false">false</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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848 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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849 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_a_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_a_ions" falsevalue="" checked="false" optional="True" label="Add peaks of a-ions to the spectrum" help="(-add_a_ions) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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850 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_c_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_c_ions" falsevalue="" checked="false" optional="True" label="Add peaks of c-ions to the spectrum" help="(-add_c_ions) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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851 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_x_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_x_ions" falsevalue="" checked="false" optional="True" label="Add peaks of x-ions to the spectrum" help="(-add_x_ions) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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852 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_z_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_z_ions" falsevalue="" checked="false" optional="True" label="Add peaks of z-ions to the spectrum" help="(-add_z_ions) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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853 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_y_intensity" type="float" value="1.0" label="Intensity of the y-ions" help="(-y_intensity) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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854 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_b_intensity" type="float" value="1.0" label="Intensity of the b-ions" help="(-b_intensity) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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855 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_a_intensity" type="float" value="1.0" label="Intensity of the a-ions" help="(-a_intensity) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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856 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_c_intensity" type="float" value="1.0" label="Intensity of the c-ions" help="(-c_intensity) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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857 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_x_intensity" type="float" value="1.0" label="Intensity of the x-ions" help="(-x_intensity) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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858 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_z_intensity" type="float" value="1.0" label="Intensity of the z-ions" help="(-z_intensity) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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859 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_relative_loss_intensity" type="float" value="0.1" label="Intensity of loss ions, in relation to the intact ion intensity" help="(-relative_loss_intensity) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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860 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_intensity" type="float" value="1.0" label="Intensity of the precursor peak" help="(-precursor_intensity) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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861 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_H2O_intensity" type="float" value="1.0" label="Intensity of the H2O loss peak of the precurso" help="(-precursor_H2O_intensity) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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862 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_NH3_intensity" type="float" value="1.0" label="Intensity of the NH3 loss peak of the precurso" help="(-precursor_NH3_intensity) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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863 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_isotopes" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_isotopes" falsevalue="" checked="false" optional="True" label="If set to 1 isotope peaks of the product ion peaks are added" help="(-add_isotopes) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
864 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_max_isotope" type="integer" value="2" label="Defines the maximal isotopic peak which is added, add_isotopes must be set to 1" help="(-max_isotope) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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865 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_metainfo" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_metainfo" falsevalue="" checked="false" optional="True" label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" help="(-add_metainfo) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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866 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_first_prefix_ion" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_first_prefix_ion" falsevalue="" checked="false" optional="True" label="If set to true e.g. b1 ions are added" help="(-add_first_prefix_ion) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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867 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_y_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y_ions" falsevalue="" checked="false" optional="True" label="Add peaks of y-ions to the spectrum" help="(-hide_y_ions) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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868 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_y2_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y2_ions" falsevalue="" checked="false" optional="True" label="Add peaks of y-ions to the spectrum" help="(-hide_y2_ions) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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869 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_b_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b_ions" falsevalue="" checked="false" optional="True" label="Add peaks of b-ions to the spectrum" help="(-hide_b_ions) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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870 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_b2_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b2_ions" falsevalue="" checked="false" optional="True" label="Add peaks of b-ions to the spectrum" help="(-hide_b2_ions) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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871 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_a_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_a_ions" falsevalue="" checked="false" optional="True" label="Add peaks of a-ions to the spectrum" help="(-hide_a_ions) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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872 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_c_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_c_ions" falsevalue="" checked="false" optional="True" label="Add peaks of c-ions to the spectrum" help="(-hide_c_ions) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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873 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_x_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_x_ions" falsevalue="" checked="false" optional="True" label="Add peaks of x-ions to the spectrum" help="(-hide_x_ions) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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874 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_z_ions" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_z_ions" falsevalue="" checked="false" optional="True" label="Add peaks of z-ions to the spectrum" help="(-hide_z_ions) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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875 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_losses" display="radio" type="boolean" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_losses" falsevalue="" checked="false" optional="True" label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" help="(-hide_losses) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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876 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_y_intensity" type="float" value="1.0" label="Intensity of the y-ions" help="(-y_intensity) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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877 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_b_intensity" type="float" value="1.0" label="Intensity of the b-ions" help="(-b_intensity) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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878 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_a_intensity" type="float" value="1.0" label="Intensity of the a-ions" help="(-a_intensity) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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879 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_c_intensity" type="float" value="1.0" label="Intensity of the c-ions" help="(-c_intensity) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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880 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_x_intensity" type="float" value="1.0" label="Intensity of the x-ions" help="(-x_intensity) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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881 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_z_intensity" type="float" value="1.0" label="Intensity of the z-ions" help="(-z_intensity) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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882 <param name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_relative_loss_intensity" type="float" value="0.1" label="Intensity of loss ions, in relation to the intact ion intensity" help="(-relative_loss_intensity) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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883 <param name="param_algorithm_MSSim_Global_ionization_type" display="radio" type="select" optional="False" value="ESI" label="Type of Ionization (MALDI or ESI)" help="(-ionization_type) ">
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884 <option value="MALDI">MALDI</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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885 <option value="ESI" selected="true">ESI</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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886 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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887 <param name="param_algorithm_MSSim_Labeling_type" type="select" optional="False" value="labelfree" label="Select the labeling type you want for your experiment" help="(-type) ">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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888 <option value="ICPL">ICPL</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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889 <option value="SILAC">SILAC</option>
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890 <option value="itraq">itraq</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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891 <option value="labelfree" selected="true">labelfree</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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892 <option value="o18">o18</option>
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893 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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894 <param name="param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift" type="float" value="0.0" label="Fixed retention time shift between labeled pairs" help="(-ICPL_fixed_rtshift) If set to 0.0 only the retention times, computed by the RT model step are used"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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895 <param name="param_algorithm_MSSim_Labeling_ICPL_label_proteins" display="radio" type="select" optional="False" value="true" label="Enables protein-labeling" help="(-label_proteins) (select 'false' if you only need peptide-labeling)">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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896 <option value="true" selected="true">true</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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897 <option value="false">false</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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898 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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899 <param name="param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift" type="float" min="0.0" optional="True" value="0.0001" label="Fixed retention time shift between labeled peptides" help="(-fixed_rtshift) If set to 0.0 only the retention times computed by the RT model step are used"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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900 <param name="param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_lysine" type="text" size="30" value="UniMod:481" label="Modification of Lysine in the medium SILAC channel" help="(-modification_lysine) ">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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901 <sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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902 <valid initial="string.printable">
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903 <remove value="'"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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904 <remove value="&quot;"/>
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diff changeset
905 </valid>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
906 </sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
907 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
908 <param name="param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_arginine" type="text" size="30" value="UniMod:188" label="Modification of Arginine in the medium SILAC channel" help="(-modification_arginine) ">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
909 <sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
910 <valid initial="string.printable">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
911 <remove value="'"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
912 <remove value="&quot;"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
913 </valid>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
914 </sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
915 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
916 <param name="param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_lysine" type="text" size="30" value="UniMod:259" label="Modification of Lysine in the heavy SILAC channel" help="(-modification_lysine) If left empty, two channelSILAC is assumed">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
917 <sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
918 <valid initial="string.printable">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
919 <remove value="'"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
920 <remove value="&quot;"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
921 </valid>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
922 </sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
923 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
924 <param name="param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine" type="text" size="30" value="UniMod:267" label="Modification of Arginine in the heavy SILAC channel" help="(-modification_arginine) If left empty, two-channel SILAC is assumed">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
925 <sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
926 <valid initial="string.printable">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
927 <remove value="'"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
928 <remove value="&quot;"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
929 </valid>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
930 </sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
931 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
932 <param name="param_algorithm_MSSim_Labeling_itraq_iTRAQ" display="radio" type="select" optional="False" value="4plex" label="4plex or 8plex iTRAQ?" help="(-iTRAQ) ">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
933 <option value="4plex" selected="true">4plex</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
934 <option value="8plex">8plex</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
935 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
936 <param name="param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift" type="float" min="0.0" max="0.5" optional="True" value="0.1" label="Allowed shift (uniformly distributed - left to right) in Da from the expected position (of" help="(-reporter_mass_shift) e.g. 114.1, 115.1)"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
937 <repeat name="rep_param_algorithm_MSSim_Labeling_itraq_channel_active_4plex" min="0" max="1" title="param_algorithm_MSSim_Labeling_itraq_channel_active_4plex">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
938 <param name="param_algorithm_MSSim_Labeling_itraq_channel_active_4plex" type="text" size="30" value="114:myReference" label="Four-plex only: Each channel that was used in the experiment and its description (114-117) in format &lt;channel&gt;:&lt;name&gt;," help="(-channel_active_4plex) e.g. &quot;114:myref&quot;,&quot;115:liver&quot;">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
939 <sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
940 <valid initial="string.printable">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
941 <remove value="'"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
942 <remove value="&quot;"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
943 </valid>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
944 </sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
945 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
946 </repeat>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
947 <repeat name="rep_param_algorithm_MSSim_Labeling_itraq_channel_active_8plex" min="0" max="1" title="param_algorithm_MSSim_Labeling_itraq_channel_active_8plex">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
948 <param name="param_algorithm_MSSim_Labeling_itraq_channel_active_8plex" type="text" size="30" value="113:myReference" label="Eight-plex only: Each channel that was used in the experiment and its description (113-121) in format &lt;channel&gt;:&lt;name&gt;," help="(-channel_active_8plex) e.g. &quot;113:myref&quot;,&quot;115:liver&quot;,&quot;118:lung&quot;">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
949 <sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
950 <valid initial="string.printable">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
951 <remove value="'"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
952 <remove value="&quot;"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
953 </valid>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
954 </sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
955 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
956 </repeat>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
957 <param name="param_algorithm_MSSim_Labeling_itraq_Y_contamination" type="float" min="0.0" max="1.0" optional="True" value="0.3" label="Efficiency of labeling tyrosine ('Y') residues" help="(-Y_contamination) 0=off, 1=full labeling"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
958 <param name="param_algorithm_MSSim_Labeling_o18_labeling_efficiency" type="float" min="0.0" max="1.0" optional="True" value="1.0" label="Describes the distribution of the labeled peptide over the different states (unlabeled, mono- and di-labeled)" help="(-labeling_efficiency) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
959 <param name="param_algorithm_RandomNumberGenerators_biological" display="radio" type="select" optional="False" value="random" label="Controls the 'biological' randomness of the generated data (" help="(-biological) e.g. systematic effects like deviations in RT). If set to 'random' each experiment will look different. If set to 'reproducible' each experiment will have the same outcome (given that the input data is the same)">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
960 <option value="reproducible">reproducible</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
961 <option value="random" selected="true">random</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
962 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
963 <param name="param_algorithm_RandomNumberGenerators_technical" display="radio" type="select" optional="False" value="random" label="Controls the 'technical' randomness of the generated data (" help="(-technical) e.g. noise in the raw signal). If set to 'random' each experiment will look different. If set to 'reproducible' each experiment will have the same outcome (given that the input data is the same)">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
964 <option value="reproducible">reproducible</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
965 <option value="random" selected="true">random</option>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
966 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
967 <expand macro="advanced_options">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
968 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
969 <param name="param_algorithm_MSSim_Ionization_esi_max_impurity_set_size" type="integer" value="3" label="Maximal #combinations of charge impurities allowed (each generating one feature) per charge state" help="(-max_impurity_set_size) E.g. assuming charge=3 and this parameter is 2, then we could choose to allow '3H+, 2H+Na+' features (given a certain 'charge_impurity' constraints), but no '3H+, 2H+Na+, 3Na+'"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
970 <param name="param_algorithm_MSSim_Labeling_ICPL_ICPL_light_channel_label" type="text" size="30" value="UniMod:365" label="UniMod Id of the light channel ICPL label" help="(-ICPL_light_channel_label) ">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
971 <sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
972 <valid initial="string.printable">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
973 <remove value="'"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
974 <remove value="&quot;"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
975 </valid>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
976 </sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
977 </param>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
978 <param name="param_algorithm_MSSim_Labeling_ICPL_ICPL_medium_channel_label" type="text" size="30" value="UniMod:687" label="UniMod Id of the medium channel ICPL label" help="(-ICPL_medium_channel_label) ">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
979 <sanitizer>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
980 <valid initial="string.printable">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
981 <remove value="'"/>
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982 <remove value="&quot;"/>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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983 </valid>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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984 </sanitizer>
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985 </param>
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986 <param name="param_algorithm_MSSim_Labeling_ICPL_ICPL_heavy_channel_label" type="text" size="30" value="UniMod:364" label="UniMod Id of the heavy channel ICPL label" help="(-ICPL_heavy_channel_label) ">
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987 <sanitizer>
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988 <valid initial="string.printable">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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989 <remove value="'"/>
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990 <remove value="&quot;"/>
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991 </valid>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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992 </sanitizer>
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993 </param>
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994 <repeat name="rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex" min="0" max="1" title="param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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995 <param name="param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex" type="text" size="30" value="114:0/1/5.9/0.2 115:0/2/5.6/0.1 116:0/3/4.5/0.1 117:0.1/4/3.5/0.1" label="override default values (see Documentation); use the following format: &lt;channel&gt;:&lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ;" help="(-isotope_correction_values_4plex) e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2' ">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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996 <sanitizer>
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997 <valid initial="string.printable">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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998 <remove value="'"/>
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999 <remove value="&quot;"/>
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1000 </valid>
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1001 </sanitizer>
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1002 </param>
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1003 </repeat>
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1004 <repeat name="rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex" min="0" max="1" title="param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex">
7c2b85eb3ccf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1005 <param name="param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex" type="text" size="30" value="113:0/0/6.89/0.22 114:0/0.94/5.9/0.16 115:0/1.88/4.9/0.1 116:0/2.82/3.9/0.07 117:0.06/3.77/2.99/0 118:0.09/4.71/1.88/0 119:0.14/5.66/0.87/0 121:0.27/7.44/0.18/0" label="override default values (see Documentation); use the following format: &lt;channel&gt;:&lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt; ;" help="(-isotope_correction_values_8plex) e.g. '113:0/0.3/4/0' , '116:0.1/0.3/3/0.2' ">
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1006 <sanitizer>
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1007 <valid initial="string.printable">
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1008 <remove value="'"/>
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1009 <remove value="&quot;"/>
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1010 </valid>
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1011 </sanitizer>
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1012 </param>
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1013 </repeat>
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1014 </expand>
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1015 </inputs>
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1016 <outputs>
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1017 <data name="param_out" format="mzml"/>
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1018 <data name="param_out_pm" format="mzml"/>
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1019 <data name="param_out_fm" format="featurexml"/>
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1020 <data name="param_out_cm" format="consensusxml"/>
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1021 <data name="param_out_lcm" format="consensusxml"/>
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1022 <data name="param_out_cntm" format="featurexml"/>
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1023 <data name="param_out_id" format="idxml"/>
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1024 </outputs>
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1025 <help>A highly configurable simulator for mass spectrometry experiments.
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1026
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1027
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1028 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MSSimulator.html</help>
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1029 </tool>