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annotate MSSimulator.xml @ 4:6ead64a594bd draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
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4
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="MSSimulator" name="MSSimulator" version="2.0.0">
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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 -threads \${GALAXY_SLOTS:-24}
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41 #if $param_algorithm_MSSim_Digestion_enzyme:
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42 -algorithm:MSSim:Digestion:enzyme
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43 #if &quot; &quot; in str($param_algorithm_MSSim_Digestion_enzyme):
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44 &quot;$param_algorithm_MSSim_Digestion_enzyme&quot;
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45 #else
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46 $param_algorithm_MSSim_Digestion_enzyme
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47 #end if
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48 #end if
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49 #if $param_algorithm_MSSim_Digestion_model:
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50 -algorithm:MSSim:Digestion:model
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51 #if &quot; &quot; in str($param_algorithm_MSSim_Digestion_model):
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52 &quot;$param_algorithm_MSSim_Digestion_model&quot;
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53 #else
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54 $param_algorithm_MSSim_Digestion_model
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55 #end if
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56 #end if
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57 #if $param_algorithm_MSSim_Digestion_min_peptide_length:
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58 -algorithm:MSSim:Digestion:min_peptide_length $param_algorithm_MSSim_Digestion_min_peptide_length
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59 #end if
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60 #if $param_algorithm_MSSim_Digestion_model_trained_threshold:
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61 -algorithm:MSSim:Digestion:model_trained:threshold $param_algorithm_MSSim_Digestion_model_trained_threshold
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62 #end if
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63 #if $param_algorithm_MSSim_Digestion_model_naive_missed_cleavages:
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64 -algorithm:MSSim:Digestion:model_naive:missed_cleavages $param_algorithm_MSSim_Digestion_model_naive_missed_cleavages
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65 #end if
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66 #if $param_algorithm_MSSim_RT_rt_column:
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67 -algorithm:MSSim:RT:rt_column
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68 #if &quot; &quot; in str($param_algorithm_MSSim_RT_rt_column):
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69 &quot;$param_algorithm_MSSim_RT_rt_column&quot;
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70 #else
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71 $param_algorithm_MSSim_RT_rt_column
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72 #end if
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73 #end if
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74 #if $param_algorithm_MSSim_RT_auto_scale:
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75 -algorithm:MSSim:RT:auto_scale
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76 #end if
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77 #if $param_algorithm_MSSim_RT_total_gradient_time:
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78 -algorithm:MSSim:RT:total_gradient_time $param_algorithm_MSSim_RT_total_gradient_time
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79 #end if
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80 #if $param_algorithm_MSSim_RT_sampling_rate:
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81 -algorithm:MSSim:RT:sampling_rate $param_algorithm_MSSim_RT_sampling_rate
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82 #end if
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83 #if $param_algorithm_MSSim_RT_scan_window_min:
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84 -algorithm:MSSim:RT:scan_window:min $param_algorithm_MSSim_RT_scan_window_min
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85 #end if
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86 #if $param_algorithm_MSSim_RT_scan_window_max:
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87 -algorithm:MSSim:RT:scan_window:max $param_algorithm_MSSim_RT_scan_window_max
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88 #end if
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89 #if $param_algorithm_MSSim_RT_variation_feature_stddev:
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90 -algorithm:MSSim:RT:variation:feature_stddev $param_algorithm_MSSim_RT_variation_feature_stddev
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91 #end if
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92 #if $param_algorithm_MSSim_RT_variation_affine_offset:
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93 -algorithm:MSSim:RT:variation:affine_offset $param_algorithm_MSSim_RT_variation_affine_offset
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94 #end if
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95 #if $param_algorithm_MSSim_RT_variation_affine_scale:
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96 -algorithm:MSSim:RT:variation:affine_scale $param_algorithm_MSSim_RT_variation_affine_scale
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97 #end if
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98 #if $param_algorithm_MSSim_RT_column_condition_distortion:
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99 -algorithm:MSSim:RT:column_condition:distortion $param_algorithm_MSSim_RT_column_condition_distortion
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100 #end if
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101 #if $param_algorithm_MSSim_RT_profile_shape_width_value:
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102 -algorithm:MSSim:RT:profile_shape:width:value $param_algorithm_MSSim_RT_profile_shape_width_value
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103 #end if
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104 #if $param_algorithm_MSSim_RT_profile_shape_width_variance:
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105 -algorithm:MSSim:RT:profile_shape:width:variance $param_algorithm_MSSim_RT_profile_shape_width_variance
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106 #end if
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107 #if $param_algorithm_MSSim_RT_profile_shape_skewness_value:
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108 -algorithm:MSSim:RT:profile_shape:skewness:value $param_algorithm_MSSim_RT_profile_shape_skewness_value
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109 #end if
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110 #if $param_algorithm_MSSim_RT_profile_shape_skewness_variance:
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111 -algorithm:MSSim:RT:profile_shape:skewness:variance $param_algorithm_MSSim_RT_profile_shape_skewness_variance
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112 #end if
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113 #if $param_algorithm_MSSim_RT_HPLC_model_file:
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114 -algorithm:MSSim:RT:HPLC:model_file &quot;$param_algorithm_MSSim_RT_HPLC_model_file&quot;
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115 #end if
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116 #if $param_algorithm_MSSim_RT_CE_pH:
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117 -algorithm:MSSim:RT:CE:pH $param_algorithm_MSSim_RT_CE_pH
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118 #end if
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119 #if $param_algorithm_MSSim_RT_CE_alpha:
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120 -algorithm:MSSim:RT:CE:alpha $param_algorithm_MSSim_RT_CE_alpha
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121 #end if
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122 #if $param_algorithm_MSSim_RT_CE_mu_eo:
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123 -algorithm:MSSim:RT:CE:mu_eo $param_algorithm_MSSim_RT_CE_mu_eo
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124 #end if
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125 #if $param_algorithm_MSSim_RT_CE_lenght_d:
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126 -algorithm:MSSim:RT:CE:lenght_d $param_algorithm_MSSim_RT_CE_lenght_d
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127 #end if
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128 #if $param_algorithm_MSSim_RT_CE_length_total:
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129 -algorithm:MSSim:RT:CE:length_total $param_algorithm_MSSim_RT_CE_length_total
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130 #end if
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131 #if $param_algorithm_MSSim_RT_CE_voltage:
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132 -algorithm:MSSim:RT:CE:voltage $param_algorithm_MSSim_RT_CE_voltage
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133 #end if
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134 #if $param_algorithm_MSSim_Detectability_dt_simulation_on:
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135 -algorithm:MSSim:Detectability:dt_simulation_on
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136 #end if
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137 #if $param_algorithm_MSSim_Detectability_min_detect:
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138 -algorithm:MSSim:Detectability:min_detect $param_algorithm_MSSim_Detectability_min_detect
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139 #end if
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140 #if $param_algorithm_MSSim_Detectability_dt_model_file:
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141 -algorithm:MSSim:Detectability:dt_model_file &quot;$param_algorithm_MSSim_Detectability_dt_model_file&quot;
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142 #end if
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143
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144 #if $rep_param_algorithm_MSSim_Ionization_esi_ionized_residues:
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145 -algorithm:MSSim:Ionization:esi:ionized_residues
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146 #for token in $rep_param_algorithm_MSSim_Ionization_esi_ionized_residues:
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147 #if &quot; &quot; in str(token):
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148 &quot;$token.param_algorithm_MSSim_Ionization_esi_ionized_residues&quot;
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149 #else
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150 $token.param_algorithm_MSSim_Ionization_esi_ionized_residues
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151 #end if
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152 #end for
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153 #end if
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154
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155 #if $rep_param_algorithm_MSSim_Ionization_esi_charge_impurity:
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156 -algorithm:MSSim:Ionization:esi:charge_impurity
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157 #for token in $rep_param_algorithm_MSSim_Ionization_esi_charge_impurity:
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158 #if &quot; &quot; in str(token):
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159 &quot;$token.param_algorithm_MSSim_Ionization_esi_charge_impurity&quot;
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160 #else
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161 $token.param_algorithm_MSSim_Ionization_esi_charge_impurity
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162 #end if
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163 #end for
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164 #end if
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165 #if $param_algorithm_MSSim_Ionization_esi_ionization_probability:
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166 -algorithm:MSSim:Ionization:esi:ionization_probability $param_algorithm_MSSim_Ionization_esi_ionization_probability
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167 #end if
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168
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169 #if $rep_param_algorithm_MSSim_Ionization_maldi_ionization_probabilities:
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170 -algorithm:MSSim:Ionization:maldi:ionization_probabilities
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171 #for token in $rep_param_algorithm_MSSim_Ionization_maldi_ionization_probabilities:
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172 #if &quot; &quot; in str(token):
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173 &quot;$token.param_algorithm_MSSim_Ionization_maldi_ionization_probabilities&quot;
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174 #else
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175 $token.param_algorithm_MSSim_Ionization_maldi_ionization_probabilities
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176 #end if
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177 #end for
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178 #end if
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179 #if $param_algorithm_MSSim_Ionization_mz_lower_measurement_limit:
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180 -algorithm:MSSim:Ionization:mz:lower_measurement_limit $param_algorithm_MSSim_Ionization_mz_lower_measurement_limit
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181 #end if
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182 #if $param_algorithm_MSSim_Ionization_mz_upper_measurement_limit:
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183 -algorithm:MSSim:Ionization:mz:upper_measurement_limit $param_algorithm_MSSim_Ionization_mz_upper_measurement_limit
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184 #end if
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185 #if $param_algorithm_MSSim_RawSignal_enabled:
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186 -algorithm:MSSim:RawSignal:enabled
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187 #end if
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188 #if $param_algorithm_MSSim_RawSignal_peak_shape:
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189 -algorithm:MSSim:RawSignal:peak_shape
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190 #if &quot; &quot; in str($param_algorithm_MSSim_RawSignal_peak_shape):
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191 &quot;$param_algorithm_MSSim_RawSignal_peak_shape&quot;
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192 #else
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193 $param_algorithm_MSSim_RawSignal_peak_shape
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194 #end if
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195 #end if
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196 #if $param_algorithm_MSSim_RawSignal_resolution_value:
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197 -algorithm:MSSim:RawSignal:resolution:value $param_algorithm_MSSim_RawSignal_resolution_value
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198 #end if
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199 #if $param_algorithm_MSSim_RawSignal_resolution_type:
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200 -algorithm:MSSim:RawSignal:resolution:type
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201 #if &quot; &quot; in str($param_algorithm_MSSim_RawSignal_resolution_type):
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202 &quot;$param_algorithm_MSSim_RawSignal_resolution_type&quot;
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203 #else
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204 $param_algorithm_MSSim_RawSignal_resolution_type
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205 #end if
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206 #end if
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207 #if $param_algorithm_MSSim_RawSignal_baseline_scaling:
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208 -algorithm:MSSim:RawSignal:baseline:scaling $param_algorithm_MSSim_RawSignal_baseline_scaling
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209 #end if
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210 #if $param_algorithm_MSSim_RawSignal_baseline_shape:
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211 -algorithm:MSSim:RawSignal:baseline:shape $param_algorithm_MSSim_RawSignal_baseline_shape
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212 #end if
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213 #if $param_algorithm_MSSim_RawSignal_mz_sampling_points:
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214 -algorithm:MSSim:RawSignal:mz:sampling_points $param_algorithm_MSSim_RawSignal_mz_sampling_points
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215 #end if
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216 #if $param_algorithm_MSSim_RawSignal_contaminants_file:
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217 -algorithm:MSSim:RawSignal:contaminants:file &quot;$param_algorithm_MSSim_RawSignal_contaminants_file&quot;
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218 #end if
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219 #if $param_algorithm_MSSim_RawSignal_variation_mz_error_stddev:
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220 -algorithm:MSSim:RawSignal:variation:mz:error_stddev $param_algorithm_MSSim_RawSignal_variation_mz_error_stddev
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221 #end if
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222 #if $param_algorithm_MSSim_RawSignal_variation_mz_error_mean:
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223 -algorithm:MSSim:RawSignal:variation:mz:error_mean $param_algorithm_MSSim_RawSignal_variation_mz_error_mean
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224 #end if
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225 #if $param_algorithm_MSSim_RawSignal_variation_intensity_scale:
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226 -algorithm:MSSim:RawSignal:variation:intensity:scale $param_algorithm_MSSim_RawSignal_variation_intensity_scale
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227 #end if
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228 #if $param_algorithm_MSSim_RawSignal_variation_intensity_scale_stddev:
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229 -algorithm:MSSim:RawSignal:variation:intensity:scale_stddev $param_algorithm_MSSim_RawSignal_variation_intensity_scale_stddev
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230 #end if
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231 #if $param_algorithm_MSSim_RawSignal_noise_shot_rate:
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232 -algorithm:MSSim:RawSignal:noise:shot:rate $param_algorithm_MSSim_RawSignal_noise_shot_rate
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233 #end if
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234 #if $param_algorithm_MSSim_RawSignal_noise_shot_intensity_mean:
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235 -algorithm:MSSim:RawSignal:noise:shot:intensity-mean $param_algorithm_MSSim_RawSignal_noise_shot_intensity_mean
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236 #end if
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237 #if $param_algorithm_MSSim_RawSignal_noise_white_mean:
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238 -algorithm:MSSim:RawSignal:noise:white:mean $param_algorithm_MSSim_RawSignal_noise_white_mean
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239 #end if
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240 #if $param_algorithm_MSSim_RawSignal_noise_white_stddev:
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241 -algorithm:MSSim:RawSignal:noise:white:stddev $param_algorithm_MSSim_RawSignal_noise_white_stddev
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242 #end if
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243 #if $param_algorithm_MSSim_RawSignal_noise_detector_mean:
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244 -algorithm:MSSim:RawSignal:noise:detector:mean $param_algorithm_MSSim_RawSignal_noise_detector_mean
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245 #end if
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246 #if $param_algorithm_MSSim_RawSignal_noise_detector_stddev:
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247 -algorithm:MSSim:RawSignal:noise:detector:stddev $param_algorithm_MSSim_RawSignal_noise_detector_stddev
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248 #end if
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249 #if $param_algorithm_MSSim_RawTandemSignal_status:
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250 -algorithm:MSSim:RawTandemSignal:status
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251 #if &quot; &quot; in str($param_algorithm_MSSim_RawTandemSignal_status):
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252 &quot;$param_algorithm_MSSim_RawTandemSignal_status&quot;
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253 #else
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254 $param_algorithm_MSSim_RawTandemSignal_status
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255 #end if
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256 #end if
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257 #if $param_algorithm_MSSim_RawTandemSignal_tandem_mode:
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258 -algorithm:MSSim:RawTandemSignal:tandem_mode $param_algorithm_MSSim_RawTandemSignal_tandem_mode
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259 #end if
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260 #if $param_algorithm_MSSim_RawTandemSignal_svm_model_set_file:
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261 -algorithm:MSSim:RawTandemSignal:svm_model_set_file &quot;$param_algorithm_MSSim_RawTandemSignal_svm_model_set_file&quot;
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262 #end if
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263 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ms2_spectra_per_rt_bin:
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264 -algorithm:MSSim:RawTandemSignal:Precursor:ms2_spectra_per_rt_bin $param_algorithm_MSSim_RawTandemSignal_Precursor_ms2_spectra_per_rt_bin
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265 #end if
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266 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_min_mz_peak_distance:
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267 -algorithm:MSSim:RawTandemSignal:Precursor:min_mz_peak_distance $param_algorithm_MSSim_RawTandemSignal_Precursor_min_mz_peak_distance
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268 #end if
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269 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_mz_isolation_window:
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270 -algorithm:MSSim:RawTandemSignal:Precursor:mz_isolation_window $param_algorithm_MSSim_RawTandemSignal_Precursor_mz_isolation_window
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271 #end if
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272 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_exclude_overlapping_peaks:
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273 -algorithm:MSSim:RawTandemSignal:Precursor:exclude_overlapping_peaks
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274 #end if
0
3d84209d3178 Uploaded
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275
4
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276 #if $rep_param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter:
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277 -algorithm:MSSim:RawTandemSignal:Precursor:charge_filter
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278 #for token in $rep_param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter:
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279 #if &quot; &quot; in str(token):
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280 &quot;$token.param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter&quot;
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281 #else
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282 $token.param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter
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283 #end if
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284 #end for
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285 #end if
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286 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_use_dynamic_exclusion:
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287 -algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:use_dynamic_exclusion
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288 #end if
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289 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_exclusion_time:
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290 -algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:exclusion_time $param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_exclusion_time
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291 #end if
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292 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_max_list_size:
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293 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:max_list_size $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_max_list_size
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294 #end if
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295 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_min_rt:
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296 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:min_rt $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_min_rt
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297 #end if
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298 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_max_rt:
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299 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:max_rt $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_max_rt
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300 #end if
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301 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_step_size:
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302 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_step_size $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_step_size
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303 #end if
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304 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_window_size:
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305 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:rt:rt_window_size $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_window_size
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306 #end if
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307 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_protein_id_probability:
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308 -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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309 #end if
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310 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_pt_weight:
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311 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_pt_weight $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_pt_weight
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312 #end if
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313 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_mz:
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314 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_mz $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_mz
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315 #end if
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316 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_max_mz:
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317 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:max_mz $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_max_mz
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318 #end if
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319 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_use_peptide_rule:
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320 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:use_peptide_rule
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321 #end if
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322 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_ids:
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323 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_ids $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_ids
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324 #end if
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325 #if $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_probability:
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326 -algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:min_peptide_probability $param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_probability
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327 #end if
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328 #if $param_algorithm_MSSim_RawTandemSignal_MS_E_add_single_spectra:
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329 -algorithm:MSSim:RawTandemSignal:MS_E:add_single_spectra
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330 #end if
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331 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_isotopes:
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332 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_isotopes
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333 #end if
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334 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_max_isotope:
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335 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:max_isotope $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_max_isotope
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336 #end if
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337 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_metainfo:
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338 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_metainfo
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339 #end if
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340 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_losses:
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341 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses
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342 #end if
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343 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_precursor_peaks:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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344 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks
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345 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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346 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_abundant_immonium_ions:
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diff changeset
347 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions
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diff changeset
348 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
349 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_first_prefix_ion:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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350 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
351 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
352 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
353 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_y_ions
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
354 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
355 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
356 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_b_ions
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
357 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
358 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_a_ions:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
359 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_a_ions
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
360 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
361 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_c_ions:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
362 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_c_ions
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
363 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
364 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_x_ions:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
365 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_x_ions
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
366 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
367 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_z_ions:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
368 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_z_ions
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
369 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
370 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_y_intensity:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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371 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:y_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_y_intensity
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
372 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
373 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_b_intensity:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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374 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:b_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_b_intensity
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
375 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
376 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_a_intensity:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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377 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:a_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_a_intensity
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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378 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
379 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_c_intensity:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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380 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:c_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_c_intensity
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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381 #end if
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diff changeset
382 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_x_intensity:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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383 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:x_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_x_intensity
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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384 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
385 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_z_intensity:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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386 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:z_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_z_intensity
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387 #end if
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diff changeset
388 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_relative_loss_intensity:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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389 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:relative_loss_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_relative_loss_intensity
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390 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
391 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_intensity:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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392 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_intensity
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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393 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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394 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_H2O_intensity:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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395 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_H2O_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_H2O_intensity
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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396 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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397 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_NH3_intensity:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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398 -algorithm:MSSim:RawTandemSignal:TandemSim:Simple:precursor_NH3_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_NH3_intensity
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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399 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
400 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_isotopes:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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401 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_isotopes
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402 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
403 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_max_isotope:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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404 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:max_isotope $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_max_isotope
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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405 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
406 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_metainfo:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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407 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_metainfo
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
408 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
409 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_first_prefix_ion:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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410 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_first_prefix_ion
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
411 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
412 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_y_ions:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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413 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y_ions
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parents: 0
diff changeset
414 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
415 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_y2_ions:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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416 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y2_ions
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
417 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
418 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_b_ions:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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419 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b_ions
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
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420 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
421 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_b2_ions:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
422 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b2_ions
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
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423 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
424 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_a_ions:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
425 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_a_ions
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
426 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
427 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_c_ions:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
428 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_c_ions
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
429 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
430 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_x_ions:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
431 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_x_ions
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
432 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
433 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_z_ions:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
434 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_z_ions
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
435 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
436 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_losses:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
437 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_losses
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
438 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
439 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_y_intensity:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
440 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:y_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_y_intensity
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
441 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
442 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_b_intensity:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
443 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:b_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_b_intensity
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
444 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
445 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_a_intensity:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
446 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:a_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_a_intensity
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
447 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
448 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_c_intensity:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
449 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:c_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_c_intensity
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
450 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
451 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_x_intensity:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
452 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:x_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_x_intensity
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
453 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
454 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_z_intensity:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
455 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:z_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_z_intensity
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
456 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
457 #if $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_relative_loss_intensity:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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458 -algorithm:MSSim:RawTandemSignal:TandemSim:SVM:relative_loss_intensity $param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_relative_loss_intensity
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
459 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
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diff changeset
460 #if $param_algorithm_MSSim_Global_ionization_type:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
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diff changeset
461 -algorithm:MSSim:Global:ionization_type
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
462 #if &quot; &quot; in str($param_algorithm_MSSim_Global_ionization_type):
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
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diff changeset
463 &quot;$param_algorithm_MSSim_Global_ionization_type&quot;
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
464 #else
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
465 $param_algorithm_MSSim_Global_ionization_type
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
466 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
467 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
468 #if $param_algorithm_MSSim_Labeling_type:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
469 -algorithm:MSSim:Labeling:type
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
470 #if &quot; &quot; in str($param_algorithm_MSSim_Labeling_type):
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
471 &quot;$param_algorithm_MSSim_Labeling_type&quot;
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
472 #else
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
473 $param_algorithm_MSSim_Labeling_type
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
474 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
475 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
476 #if $param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
477 -algorithm:MSSim:Labeling:ICPL:ICPL_fixed_rtshift $param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
478 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
479 #if $param_algorithm_MSSim_Labeling_ICPL_label_proteins:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
480 -algorithm:MSSim:Labeling:ICPL:label_proteins
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
481 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
482 #if $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
483 -algorithm:MSSim:Labeling:SILAC:fixed_rtshift $param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
484 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
485 #if $param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_lysine:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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486 -algorithm:MSSim:Labeling:SILAC:medium_channel:modification_lysine &quot;$param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_lysine&quot;
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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487 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
488 #if $param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_arginine:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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489 -algorithm:MSSim:Labeling:SILAC:medium_channel:modification_arginine &quot;$param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_arginine&quot;
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
490 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
491 #if $param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_lysine:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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492 -algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_lysine &quot;$param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_lysine&quot;
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
493 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
494 #if $param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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495 -algorithm:MSSim:Labeling:SILAC:heavy_channel:modification_arginine &quot;$param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine&quot;
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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496 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
497 #if $param_algorithm_MSSim_Labeling_itraq_iTRAQ:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
498 -algorithm:MSSim:Labeling:itraq:iTRAQ
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
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diff changeset
499 #if &quot; &quot; in str($param_algorithm_MSSim_Labeling_itraq_iTRAQ):
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
500 &quot;$param_algorithm_MSSim_Labeling_itraq_iTRAQ&quot;
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
501 #else
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
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diff changeset
502 $param_algorithm_MSSim_Labeling_itraq_iTRAQ
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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503 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
504 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
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diff changeset
505 #if $param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
506 -algorithm:MSSim:Labeling:itraq:reporter_mass_shift $param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
507 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
508
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
509 #if $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_4plex:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
510 -algorithm:MSSim:Labeling:itraq:channel_active_4plex
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
511 #for token in $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_4plex:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
512 #if &quot; &quot; in str(token):
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
513 &quot;$token.param_algorithm_MSSim_Labeling_itraq_channel_active_4plex&quot;
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
514 #else
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bgruening
parents: 0
diff changeset
515 $token.param_algorithm_MSSim_Labeling_itraq_channel_active_4plex
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
516 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
517 #end for
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
518 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
519
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
520 #if $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_8plex:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
521 -algorithm:MSSim:Labeling:itraq:channel_active_8plex
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
522 #for token in $rep_param_algorithm_MSSim_Labeling_itraq_channel_active_8plex:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
523 #if &quot; &quot; in str(token):
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
524 &quot;$token.param_algorithm_MSSim_Labeling_itraq_channel_active_8plex&quot;
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
525 #else
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
526 $token.param_algorithm_MSSim_Labeling_itraq_channel_active_8plex
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
527 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
528 #end for
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
529 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
530 #if $param_algorithm_MSSim_Labeling_itraq_Y_contamination:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
531 -algorithm:MSSim:Labeling:itraq:Y_contamination $param_algorithm_MSSim_Labeling_itraq_Y_contamination
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
532 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
533 #if $param_algorithm_MSSim_Labeling_o18_labeling_efficiency:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
534 -algorithm:MSSim:Labeling:o18:labeling_efficiency $param_algorithm_MSSim_Labeling_o18_labeling_efficiency
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
535 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
536 #if $param_algorithm_RandomNumberGenerators_biological:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
537 -algorithm:RandomNumberGenerators:biological
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
538 #if &quot; &quot; in str($param_algorithm_RandomNumberGenerators_biological):
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
539 &quot;$param_algorithm_RandomNumberGenerators_biological&quot;
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
540 #else
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
541 $param_algorithm_RandomNumberGenerators_biological
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
542 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
543 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
544 #if $param_algorithm_RandomNumberGenerators_technical:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
545 -algorithm:RandomNumberGenerators:technical
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
546 #if &quot; &quot; in str($param_algorithm_RandomNumberGenerators_technical):
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
547 &quot;$param_algorithm_RandomNumberGenerators_technical&quot;
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
548 #else
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
549 $param_algorithm_RandomNumberGenerators_technical
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
550 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
551 #end if
0
3d84209d3178 Uploaded
bgruening
parents:
diff changeset
552 #if $adv_opts.adv_opts_selector=='advanced':
4
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
553 #if $adv_opts.param_force:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
554 -force
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
555 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
556 #if $adv_opts.param_algorithm_MSSim_Ionization_esi_max_impurity_set_size:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
557 -algorithm:MSSim:Ionization:esi:max_impurity_set_size $adv_opts.param_algorithm_MSSim_Ionization_esi_max_impurity_set_size
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
558 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
559 #if $adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_light_channel_label:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
560 -algorithm:MSSim:Labeling:ICPL:ICPL_light_channel_label &quot;$adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_light_channel_label&quot;
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
561 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
562 #if $adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_medium_channel_label:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
563 -algorithm:MSSim:Labeling:ICPL:ICPL_medium_channel_label &quot;$adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_medium_channel_label&quot;
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
564 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
565 #if $adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_heavy_channel_label:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
566 -algorithm:MSSim:Labeling:ICPL:ICPL_heavy_channel_label &quot;$adv_opts.param_algorithm_MSSim_Labeling_ICPL_ICPL_heavy_channel_label&quot;
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
567 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
568
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
569 #if $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
570 -algorithm:MSSim:Labeling:itraq:isotope_correction_values_4plex
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
571 #for token in $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
572 #if &quot; &quot; in str(token):
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
573 &quot;$token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex&quot;
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
574 #else
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
575 $token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
576 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
577 #end for
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
578 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
579
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
580 #if $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
581 -algorithm:MSSim:Labeling:itraq:isotope_correction_values_8plex
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
582 #for token in $rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex:
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
583 #if &quot; &quot; in str(token):
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
584 &quot;$token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex&quot;
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
585 #else
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
586 $token.param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
587 #end if
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
588 #end for
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
589 #end if
0
3d84209d3178 Uploaded
bgruening
parents:
diff changeset
590 #end if
3d84209d3178 Uploaded
bgruening
parents:
diff changeset
591 </command>
4
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
592 <inputs>
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bgruening
parents: 0
diff changeset
593 <param format="fasta" help="(-in) " label="Input protein sequences" multiple="true" name="param_in" optional="False" size="30" type="data">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
594 <sanitizer>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
595 <valid initial="string.printable">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
596 <remove value="'"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
597 <remove value="&quot;"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
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598 </valid>
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599 </sanitizer>
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600 </param>
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601 <param help="(-enzyme) " label="Enzyme to use for digestion (select 'no cleavage' to skip digestion)" name="param_algorithm_MSSim_Digestion_enzyme" optional="True" type="select" value="Trypsin">
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602 <option value="no cleavage">no cleavage</option>
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603 <option value="V8-E">V8-E</option>
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604 <option value="Trypsin/P">Trypsin/P</option>
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605 <option value="Lys-C/P">Lys-C/P</option>
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606 <option value="unspecific cleavage">unspecific cleavage</option>
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607 <option value="leukocyte elastase">leukocyte elastase</option>
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608 <option value="proline endopeptidase">proline endopeptidase</option>
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609 <option value="V8-DE">V8-DE</option>
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610 <option value="Chymotrypsin">Chymotrypsin</option>
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611 <option value="Asp-N">Asp-N</option>
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612 <option value="2-iodobenzoate">2-iodobenzoate</option>
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613 <option value="Arg-C">Arg-C</option>
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614 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
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615 <option value="TrypChymo">TrypChymo</option>
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616 <option value="Trypsin">Trypsin</option>
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617 <option value="Formic_acid">Formic_acid</option>
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618 <option value="CNBr">CNBr</option>
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619 <option value="Asp-N_ambic">Asp-N_ambic</option>
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620 <option value="PepsinA">PepsinA</option>
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621 <option value="Lys-C">Lys-C</option>
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622 </param>
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623 <param help="(-model) 'Trained' is based on a log likelihood model (see DOI:10.1021/pr060507u)" label="The cleavage model to use for digestion" name="param_algorithm_MSSim_Digestion_model" optional="True" type="select" value="naive">
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624 <option value="trained">trained</option>
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625 <option value="naive">naive</option>
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626 </param>
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627 <param help="(-min_peptide_length) " label="Minimum peptide length after digestion (shorter ones will be discarded)" min="1" name="param_algorithm_MSSim_Digestion_min_peptide_length" optional="True" type="integer" value="3"/>
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628 <param help="(-threshold) Higher values increase the number of cleavages. -2 will give no cleavages, +4 almost full cleavage" label="Model threshold for calling a cleavage" max="4.0" min="-2.0" name="param_algorithm_MSSim_Digestion_model_trained_threshold" optional="True" type="float" value="0.5"/>
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629 <param help="(-missed_cleavages) All possible resulting peptides will be created" label="Maximum number of missed cleavages considered" min="0" name="param_algorithm_MSSim_Digestion_model_naive_missed_cleavages" optional="True" type="integer" value="1"/>
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630 <param help="(-rt_column) " label="Modelling of an RT or CE column" name="param_algorithm_MSSim_RT_rt_column" optional="True" type="select" value="HPLC">
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631 <option value="none">none</option>
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632 <option value="HPLC">HPLC</option>
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633 <option value="CE">CE</option>
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634 </param>
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635 <param checked="true" falsevalue="" help="(-auto_scale) If 'true', for CE this means that 'CE:lenght_d', 'CE:length_total', 'CE:voltage' have no influence" label="Scale predicted RT's/MT's to given 'total_gradient_time'?" name="param_algorithm_MSSim_RT_auto_scale" optional="True" truevalue="-algorithm:MSSim:RT:auto_scale" type="boolean"/>
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636 <param help="(-total_gradient_time) " label="The duration [s] of the gradient" min="1e-05" name="param_algorithm_MSSim_RT_total_gradient_time" optional="True" type="float" value="2500.0"/>
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637 <param help="(-sampling_rate) " label="Time interval [s] between consecutive scans" max="60.0" min="0.01" name="param_algorithm_MSSim_RT_sampling_rate" optional="True" type="float" value="2.0"/>
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638 <param help="(-min) " label="Start of RT Scan Window [s]" min="0.0" name="param_algorithm_MSSim_RT_scan_window_min" optional="True" type="float" value="500.0"/>
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639 <param help="(-max) " label="End of RT Scan Window [s]" min="1.0" name="param_algorithm_MSSim_RT_scan_window_max" optional="True" type="float" value="1500.0"/>
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640 <param help="(-feature_stddev) " label="Standard deviation of shift in retention time [s] from predicted model (applied to every single feature independently)" name="param_algorithm_MSSim_RT_variation_feature_stddev" type="integer" value="3"/>
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641 <param help="(-affine_offset) " label="Global offset in retention time [s] from predicted model" name="param_algorithm_MSSim_RT_variation_affine_offset" type="integer" value="0"/>
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642 <param help="(-affine_scale) " label="Global scaling in retention time from predicted model" name="param_algorithm_MSSim_RT_variation_affine_scale" type="integer" value="1"/>
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643 <param help="(-distortion) e.g. Orbitrap) distortion should be &gt;4" 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 (" max="10" min="0" name="param_algorithm_MSSim_RT_column_condition_distortion" optional="True" type="integer" value="0"/>
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644 <param help="(-value) This does not correspond directly to the width in [s]" label="Width of the Exponential Gaussian Hybrid distribution shape of the elution profile" min="0.0" name="param_algorithm_MSSim_RT_profile_shape_width_value" optional="True" type="float" value="9.0"/>
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645 <param help="(-variance) scale parameter for the lorentzian variation of the variance (Note: The scale parameter has to be &gt;= 0)" label="Random component of the width (set to 0 to disable randomness), i.e" min="0.0" name="param_algorithm_MSSim_RT_profile_shape_width_variance" optional="True" type="float" value="1.6"/>
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646 <param 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" label="Asymmetric component of the EGH" name="param_algorithm_MSSim_RT_profile_shape_skewness_value" type="float" value="0.1"/>
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647 <param help="(-variance) scale parameter for the lorentzian variation of the time constant (Note: The scale parameter has to be &gt; 0)" label="Random component of skewness (set to 0 to disable randomness), i.e" min="0.0" name="param_algorithm_MSSim_RT_profile_shape_skewness_variance" optional="True" type="float" value="0.3"/>
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648 <param help="(-model_file) " label="SVM model for retention time prediction" name="param_algorithm_MSSim_RT_HPLC_model_file" size="30" type="text" value="examples/simulation/RTPredict.model">
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649 <sanitizer>
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650 <valid initial="string.printable">
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651 <remove value="'"/>
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652 <remove value="&quot;"/>
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653 </valid>
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654 </sanitizer>
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655 </param>
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656 <param help="(-pH) " label="pH of buffe" max="14.0" min="0.0" name="param_algorithm_MSSim_RT_CE_pH" optional="True" type="float" value="3.0"/>
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657 <param help="(-alpha) " label="Exponent Alpha used to calculate mobility" max="1.0" min="0.0" name="param_algorithm_MSSim_RT_CE_alpha" optional="True" type="float" value="0.5"/>
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658 <param help="(-mu_eo) " label="Electroosmotic flow" max="5.0" min="0.0" name="param_algorithm_MSSim_RT_CE_mu_eo" optional="True" type="float" value="0.0"/>
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659 <param help="(-lenght_d) " label="Length of capillary [cm] from injection site to MS" max="1000.0" min="0.0" name="param_algorithm_MSSim_RT_CE_lenght_d" optional="True" type="float" value="70.0"/>
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660 <param help="(-length_total) " label="Total length of capillary [cm]" max="1000.0" min="0.0" name="param_algorithm_MSSim_RT_CE_length_total" optional="True" type="float" value="75.0"/>
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661 <param help="(-voltage) " label="Voltage applied to capillary" min="0.0" name="param_algorithm_MSSim_RT_CE_voltage" optional="True" type="float" value="1000.0"/>
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662 <param checked="false" falsevalue="" help="(-dt_simulation_on) This can serve as a filter to remove peptides which ionize badly, thus reducing peptide count" label="Modelling detectibility enabled?" name="param_algorithm_MSSim_Detectability_dt_simulation_on" optional="True" truevalue="-algorithm:MSSim:Detectability:dt_simulation_on" type="boolean"/>
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663 <param help="(-min_detect) Peptides with a lower score will be removed" label="Minimum peptide detectability accepted" name="param_algorithm_MSSim_Detectability_min_detect" type="float" value="0.5"/>
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664 <param help="(-dt_model_file) " label="SVM model for peptide detectability prediction" name="param_algorithm_MSSim_Detectability_dt_model_file" size="30" type="text" value="examples/simulation/DTPredict.model">
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665 <sanitizer>
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666 <valid initial="string.printable">
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667 <remove value="'"/>
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668 <remove value="&quot;"/>
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669 </valid>
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670 </sanitizer>
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671 </param>
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672 <repeat max="1" min="0" name="rep_param_algorithm_MSSim_Ionization_esi_ionized_residues" title="param_algorithm_MSSim_Ionization_esi_ionized_residues">
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673 <param help="(-ionized_residues) The N-term is always assumed to carry a charge. This parameter will be ignored during MALDI ionization" label="List of residues (as three letter code) that will be considered during ES ionization" name="param_algorithm_MSSim_Ionization_esi_ionized_residues" optional="True" type="select" value="Arg Lys His">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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674 <option value="Ala">Ala</option>
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675 <option value="Cys">Cys</option>
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676 <option value="Asp">Asp</option>
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677 <option value="Glu">Glu</option>
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678 <option value="Phe">Phe</option>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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679 <option value="Gly">Gly</option>
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680 <option value="His">His</option>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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681 <option value="Ile">Ile</option>
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682 <option value="Lys">Lys</option>
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683 <option value="Leu">Leu</option>
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684 <option value="Met">Met</option>
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685 <option value="Asn">Asn</option>
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686 <option value="Pro">Pro</option>
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687 <option value="Gln">Gln</option>
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688 <option value="Arg">Arg</option>
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689 <option value="Sec">Sec</option>
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690 <option value="Ser">Ser</option>
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691 <option value="Thr">Thr</option>
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692 <option value="Val">Val</option>
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693 <option value="Trp">Trp</option>
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694 <option value="Tyr">Tyr</option>
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695 </param>
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696 </repeat>
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697 <repeat max="1" min="0" name="rep_param_algorithm_MSSim_Ionization_esi_charge_impurity" title="param_algorithm_MSSim_Ionization_esi_charge_impurity">
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698 <param 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'])" label="List of charged ions that contribute to charge with weight of occurrence (their sum is scaled to 1 internally)," name="param_algorithm_MSSim_Ionization_esi_charge_impurity" size="30" type="text" value="H+:1">
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699 <sanitizer>
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700 <valid initial="string.printable">
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701 <remove value="'"/>
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702 <remove value="&quot;"/>
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703 </valid>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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704 </sanitizer>
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705 </param>
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706 </repeat>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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707 <param help="(-ionization_probability) " label="Probability for the binomial distribution of the ESI charge states" name="param_algorithm_MSSim_Ionization_esi_ionization_probability" type="float" value="0.8"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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708 <repeat max="1" min="0" name="rep_param_algorithm_MSSim_Ionization_maldi_ionization_probabilities" title="param_algorithm_MSSim_Ionization_maldi_ionization_probabilities">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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709 <param help="(-ionization_probabilities) " label="List of probabilities for the different charge states during MALDI ionization (the list must sum up to 1.0)" name="param_algorithm_MSSim_Ionization_maldi_ionization_probabilities" size="30" type="text" value="0.9 0.1">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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710 <sanitizer>
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711 <valid initial="string.printable">
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712 <remove value="'"/>
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713 <remove value="&quot;"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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714 </valid>
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715 </sanitizer>
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716 </param>
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717 </repeat>
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718 <param help="(-lower_measurement_limit) " label="Lower m/z detector limit" min="0.0" name="param_algorithm_MSSim_Ionization_mz_lower_measurement_limit" optional="True" type="float" value="200.0"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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719 <param help="(-upper_measurement_limit) " label="Upper m/z detector limit" min="0.0" name="param_algorithm_MSSim_Ionization_mz_upper_measurement_limit" optional="True" type="float" value="2500.0"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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720 <param checked="true" falsevalue="" help="(-enabled) (select 'false' if you only need feature-maps)" label="Enable RAW signal simulation?" name="param_algorithm_MSSim_RawSignal_enabled" optional="True" truevalue="-algorithm:MSSim:RawSignal:enabled" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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721 <param help="(-peak_shape) " 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" name="param_algorithm_MSSim_RawSignal_peak_shape" optional="True" type="select" value="Gaussian">
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722 <option value="Gaussian">Gaussian</option>
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723 <option value="Lorentzian">Lorentzian</option>
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724 </param>
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725 <param help="(-value) " label="Instrument resolution at 400 Th" name="param_algorithm_MSSim_RawSignal_resolution_value" type="integer" value="50000"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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726 <param help="(-type) " 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" name="param_algorithm_MSSim_RawSignal_resolution_type" optional="True" type="select" value="linear">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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727 <option value="constant">constant</option>
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728 <option value="linear">linear</option>
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729 <option value="sqrt">sqrt</option>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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730 </param>
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731 <param help="(-scaling) Set to 0 to disable simulation of baseline" label="Scale of baseline" min="0.0" name="param_algorithm_MSSim_RawSignal_baseline_scaling" optional="True" type="float" value="0.0"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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732 <param help="(-shape) " label="The baseline is modeled by an exponential probability density function (pdf) with f(x) = shape*e^(- shape*x)" min="0.0" name="param_algorithm_MSSim_RawSignal_baseline_shape" optional="True" type="float" value="0.5"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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733 <param help="(-sampling_points) " label="Number of raw data points per FWHM of the peak" min="2" name="param_algorithm_MSSim_RawSignal_mz_sampling_points" optional="True" type="integer" value="3"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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734 <param help="(-file) See 'OpenMS/examples/simulation/contaminants.txt' for details" label="Contaminants file with sum formula and absolute RT interval" name="param_algorithm_MSSim_RawSignal_contaminants_file" size="30" type="text" value="examples/simulation/contaminants.csv">
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735 <sanitizer>
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736 <valid initial="string.printable">
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737 <remove value="'"/>
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738 <remove value="&quot;"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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739 </valid>
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740 </sanitizer>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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741 </param>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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742 <param help="(-error_stddev) Set to 0 to disable simulation of m/z errors" label="Standard deviation for m/z errors" name="param_algorithm_MSSim_RawSignal_variation_mz_error_stddev" type="float" value="0.0"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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743 <param help="(-error_mean) " label="Average systematic m/z error (Da)" name="param_algorithm_MSSim_RawSignal_variation_mz_error_mean" type="float" value="0.0"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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744 <param help="(-scale) Set to 1.0 to get the real intensity values provided in the FASTA file" label="Constant scale factor of the feature intensity" min="0.0" name="param_algorithm_MSSim_RawSignal_variation_intensity_scale" optional="True" type="float" value="100.0"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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745 <param help="(-scale_stddev) Set to 0 to get simple rescaled intensities" label="Standard deviation of peak intensity (relative to the scaled peak height)" min="0.0" name="param_algorithm_MSSim_RawSignal_variation_intensity_scale_stddev" optional="True" type="float" value="0.0"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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746 <param help="(-rate) Set this to 0 to disable simulation of shot noise" label="Poisson rate of shot noise per unit m/z" min="0.0" name="param_algorithm_MSSim_RawSignal_noise_shot_rate" optional="True" type="float" value="0.0"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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747 <param help="(-intensity-mean) " label="Shot noise intensity mean (exponentially distributed with given mean)" name="param_algorithm_MSSim_RawSignal_noise_shot_intensity_mean" type="float" value="1.0"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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748 <param help="(-mean) " label="Mean value of white noise being added to each measured signal" name="param_algorithm_MSSim_RawSignal_noise_white_mean" type="float" value="0.0"/>
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749 <param help="(-stddev) " label="Standard deviation of white noise being added to each measured signal" name="param_algorithm_MSSim_RawSignal_noise_white_stddev" type="float" value="0.0"/>
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750 <param help="(-mean) " label="Mean value of the detector noise being added to the complete measurement" name="param_algorithm_MSSim_RawSignal_noise_detector_mean" type="float" value="0.0"/>
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751 <param help="(-stddev) " label="Standard deviation of the detector noise being added to the complete measurement" name="param_algorithm_MSSim_RawSignal_noise_detector_stddev" type="float" value="0.0"/>
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752 <param help="(-status) " label="Create Tandem-MS scans?" name="param_algorithm_MSSim_RawTandemSignal_status" optional="True" type="select" value="disabled">
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753 <option value="disabled">disabled</option>
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754 <option value="precursor">precursor</option>
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755 <option value="MS^E">MS^E</option>
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756 </param>
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757 <param help="(-tandem_mode) 0 - fixed intensities, 1 - SVC prediction (abundant/missing), 2 - SVR prediction of peak intensity &lt;br&gt;" label="Algorithm to generate the tandem-MS spectra" max="2" min="0" name="param_algorithm_MSSim_RawTandemSignal_tandem_mode" optional="True" type="integer" value="0"/>
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758 <param help="(-svm_model_set_file) " label="File containing the filenames of SVM Models for different charge variants" name="param_algorithm_MSSim_RawTandemSignal_svm_model_set_file" size="30" type="text" value="examples/simulation/SvmModelSet.model">
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759 <sanitizer>
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760 <valid initial="string.printable">
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761 <remove value="'"/>
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762 <remove value="&quot;"/>
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763 </valid>
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764 </sanitizer>
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765 </param>
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766 <param help="(-ms2_spectra_per_rt_bin) " label="Number of allowed MS/MS spectra in a retention time bin" min="1" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ms2_spectra_per_rt_bin" optional="True" type="integer" value="5"/>
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767 <param 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" label="The minimal distance (in Th) between two peaks for concurrent selection for fragmentation" min="0.0001" name="param_algorithm_MSSim_RawTandemSignal_Precursor_min_mz_peak_distance" optional="True" type="float" value="2.0"/>
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768 <param help="(-mz_isolation_window) " label="All peaks within a mass window (in Th) of a selected peak are also selected for fragmentation" min="0.0" name="param_algorithm_MSSim_RawTandemSignal_Precursor_mz_isolation_window" optional="True" type="float" value="2.0"/>
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769 <param checked="false" falsevalue="" help="(-exclude_overlapping_peaks) " label="If true, overlapping or nearby peaks (within 'min_mz_peak_distance') are excluded for selection" name="param_algorithm_MSSim_RawTandemSignal_Precursor_exclude_overlapping_peaks" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:Precursor:exclude_overlapping_peaks" type="boolean"/>
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770 <repeat max="1" min="0" name="rep_param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter" title="param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter">
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771 <param help="(-charge_filter) " label="Charges considered for MS2 fragmentation" max="5" min="1" name="param_algorithm_MSSim_RawTandemSignal_Precursor_charge_filter" optional="True" size="30" type="text" value="2 3">
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772 <sanitizer>
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773 <valid initial="string.printable">
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774 <remove value="'"/>
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775 <remove value="&quot;"/>
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776 </valid>
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777 </sanitizer>
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778 </param>
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779 </repeat>
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780 <param checked="false" falsevalue="" help="(-use_dynamic_exclusion) " label="If true dynamic exclusion is applied" name="param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_use_dynamic_exclusion" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:Precursor:Exclusion:use_dynamic_exclusion" type="boolean"/>
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781 <param help="(-exclusion_time) " label="The time (in seconds) a feature is excluded" min="0.0" name="param_algorithm_MSSim_RawTandemSignal_Precursor_Exclusion_exclusion_time" optional="True" type="float" value="100.0"/>
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782 <param help="(-max_list_size) " label="The maximal number of precursors in the inclusion list" min="1" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_max_list_size" optional="True" type="integer" value="1000"/>
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783 <param help="(-min_rt) " label="Minimal rt in seconds" min="0.0" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_min_rt" optional="True" type="float" value="960.0"/>
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784 <param help="(-max_rt) " label="Maximal rt in seconds" min="0.0" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_max_rt" optional="True" type="float" value="3840.0"/>
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785 <param help="(-rt_step_size) " label="rt step size in seconds" min="1.0" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_step_size" optional="True" type="float" value="30.0"/>
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786 <param help="(-rt_window_size) " label="rt window size in seconds" min="1" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_rt_rt_window_size" optional="True" type="integer" value="100"/>
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787 <param help="(-min_protein_id_probability) " label="Minimal protein probability for a protein to be considered identified" max="1.0" min="0.0" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_protein_id_probability" optional="True" type="float" value="0.95"/>
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788 <param help="(-min_pt_weight) " label="Minimal pt weight of a precurso" max="1.0" min="0.0" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_pt_weight" optional="True" type="float" value="0.5"/>
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789 <param help="(-min_mz) " label="Minimal mz to be considered in protein based LP formulation" min="0.0" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_mz" optional="True" type="float" value="500.0"/>
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790 <param help="(-max_mz) " label="Minimal mz to be considered in protein based LP formulation" min="0.0" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_max_mz" optional="True" type="float" value="5000.0"/>
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791 <param checked="false" falsevalue="" help="(-use_peptide_rule) " label="Use peptide rule instead of minimal protein id probability" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_use_peptide_rule" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:Precursor:ProteinBasedInclusion:thresholds:use_peptide_rule" type="boolean"/>
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792 <param help="(-min_peptide_ids) " label="If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id" min="1" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_ids" optional="True" type="integer" value="2"/>
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793 <param help="(-min_peptide_probability) " label="If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified" max="1.0" min="0.0" name="param_algorithm_MSSim_RawTandemSignal_Precursor_ProteinBasedInclusion_thresholds_min_peptide_probability" optional="True" type="float" value="0.95"/>
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794 <param checked="false" falsevalue="" 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" label="If true, the MS2 spectra for each peptide signal are included in the output (might be a lot)" name="param_algorithm_MSSim_RawTandemSignal_MS_E_add_single_spectra" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:MS_E:add_single_spectra" type="boolean"/>
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795 <param checked="false" falsevalue="" help="(-add_isotopes) " label="If set to 1 isotope peaks of the product ion peaks are added" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_isotopes" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_isotopes" type="boolean"/>
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796 <param help="(-max_isotope) " label="Defines the maximal isotopic peak which is added, add_isotopes must be set to 1" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_max_isotope" type="integer" value="2"/>
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797 <param checked="false" falsevalue="" help="(-add_metainfo) " label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_metainfo" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_metainfo" type="boolean"/>
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798 <param checked="false" falsevalue="" help="(-add_losses) " label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_losses" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_losses" type="boolean"/>
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799 <param checked="false" falsevalue="" help="(-add_precursor_peaks) " label="Adds peaks of the precursor to the spectrum, which happen to occur sometimes" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_precursor_peaks" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_precursor_peaks" type="boolean"/>
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800 <param checked="false" falsevalue="" help="(-add_abundant_immonium_ions) " label="Add most abundant immonium ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_abundant_immonium_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_abundant_immonium_ions" type="boolean"/>
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801 <param checked="false" falsevalue="" help="(-add_first_prefix_ion) " label="If set to true e.g. b1 ions are added" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_first_prefix_ion" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_first_prefix_ion" type="boolean"/>
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802 <param checked="true" falsevalue="" help="(-add_y_ions) " label="Add peaks of y-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_y_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_y_ions" type="boolean"/>
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803 <param checked="true" falsevalue="" help="(-add_b_ions) " label="Add peaks of b-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_b_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_b_ions" type="boolean"/>
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804 <param checked="false" falsevalue="" help="(-add_a_ions) " label="Add peaks of a-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_a_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_a_ions" type="boolean"/>
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805 <param checked="false" falsevalue="" help="(-add_c_ions) " label="Add peaks of c-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_c_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_c_ions" type="boolean"/>
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806 <param checked="false" falsevalue="" help="(-add_x_ions) " label="Add peaks of x-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_x_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_x_ions" type="boolean"/>
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807 <param checked="false" falsevalue="" help="(-add_z_ions) " label="Add peaks of z-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_add_z_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:Simple:add_z_ions" type="boolean"/>
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808 <param help="(-y_intensity) " label="Intensity of the y-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_y_intensity" type="float" value="1.0"/>
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809 <param help="(-b_intensity) " label="Intensity of the b-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_b_intensity" type="float" value="1.0"/>
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810 <param help="(-a_intensity) " label="Intensity of the a-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_a_intensity" type="float" value="1.0"/>
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811 <param help="(-c_intensity) " label="Intensity of the c-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_c_intensity" type="float" value="1.0"/>
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812 <param help="(-x_intensity) " label="Intensity of the x-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_x_intensity" type="float" value="1.0"/>
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813 <param help="(-z_intensity) " label="Intensity of the z-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_z_intensity" type="float" value="1.0"/>
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814 <param help="(-relative_loss_intensity) " label="Intensity of loss ions, in relation to the intact ion intensity" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_relative_loss_intensity" type="float" value="0.1"/>
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815 <param help="(-precursor_intensity) " label="Intensity of the precursor peak" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_intensity" type="float" value="1.0"/>
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816 <param help="(-precursor_H2O_intensity) " label="Intensity of the H2O loss peak of the precurso" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_H2O_intensity" type="float" value="1.0"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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817 <param help="(-precursor_NH3_intensity) " label="Intensity of the NH3 loss peak of the precurso" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_Simple_precursor_NH3_intensity" type="float" value="1.0"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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818 <param checked="false" falsevalue="" help="(-add_isotopes) " label="If set to 1 isotope peaks of the product ion peaks are added" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_isotopes" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_isotopes" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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819 <param help="(-max_isotope) " label="Defines the maximal isotopic peak which is added, add_isotopes must be set to 1" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_max_isotope" type="integer" value="2"/>
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820 <param checked="false" falsevalue="" help="(-add_metainfo) " label="Adds the type of peaks as metainfo to the peaks, like y8+, [M-H2O+2H]++" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_metainfo" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_metainfo" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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821 <param checked="false" falsevalue="" help="(-add_first_prefix_ion) " label="If set to true e.g. b1 ions are added" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_add_first_prefix_ion" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:add_first_prefix_ion" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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822 <param checked="false" falsevalue="" help="(-hide_y_ions) " label="Add peaks of y-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_y_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y_ions" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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823 <param checked="false" falsevalue="" help="(-hide_y2_ions) " label="Add peaks of y-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_y2_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_y2_ions" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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824 <param checked="false" falsevalue="" help="(-hide_b_ions) " label="Add peaks of b-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_b_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b_ions" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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825 <param checked="false" falsevalue="" help="(-hide_b2_ions) " label="Add peaks of b-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_b2_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_b2_ions" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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826 <param checked="false" falsevalue="" help="(-hide_a_ions) " label="Add peaks of a-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_a_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_a_ions" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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827 <param checked="false" falsevalue="" help="(-hide_c_ions) " label="Add peaks of c-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_c_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_c_ions" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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828 <param checked="false" falsevalue="" help="(-hide_x_ions) " label="Add peaks of x-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_x_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_x_ions" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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829 <param checked="false" falsevalue="" help="(-hide_z_ions) " label="Add peaks of z-ions to the spectrum" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_z_ions" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_z_ions" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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830 <param checked="false" falsevalue="" help="(-hide_losses) " label="Adds common losses to those ion expect to have them, only water and ammonia loss is considered" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_hide_losses" optional="True" truevalue="-algorithm:MSSim:RawTandemSignal:TandemSim:SVM:hide_losses" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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831 <param help="(-y_intensity) " label="Intensity of the y-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_y_intensity" type="float" value="1.0"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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832 <param help="(-b_intensity) " label="Intensity of the b-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_b_intensity" type="float" value="1.0"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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833 <param help="(-a_intensity) " label="Intensity of the a-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_a_intensity" type="float" value="1.0"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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834 <param help="(-c_intensity) " label="Intensity of the c-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_c_intensity" type="float" value="1.0"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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835 <param help="(-x_intensity) " label="Intensity of the x-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_x_intensity" type="float" value="1.0"/>
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836 <param help="(-z_intensity) " label="Intensity of the z-ions" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_z_intensity" type="float" value="1.0"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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837 <param help="(-relative_loss_intensity) " label="Intensity of loss ions, in relation to the intact ion intensity" name="param_algorithm_MSSim_RawTandemSignal_TandemSim_SVM_relative_loss_intensity" type="float" value="0.1"/>
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838 <param help="(-ionization_type) " label="Type of Ionization (MALDI or ESI)" name="param_algorithm_MSSim_Global_ionization_type" optional="True" type="select" value="ESI">
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839 <option value="MALDI">MALDI</option>
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840 <option value="ESI">ESI</option>
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841 </param>
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842 <param help="(-type) " label="Select the labeling type you want for your experiment" name="param_algorithm_MSSim_Labeling_type" optional="True" type="select" value="labelfree">
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843 <option value="ICPL">ICPL</option>
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844 <option value="SILAC">SILAC</option>
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845 <option value="itraq">itraq</option>
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846 <option value="labelfree">labelfree</option>
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847 <option value="o18">o18</option>
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848 </param>
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849 <param help="(-ICPL_fixed_rtshift) If set to 0.0 only the retention times, computed by the RT model step are used" label="Fixed retention time shift between labeled pairs" name="param_algorithm_MSSim_Labeling_ICPL_ICPL_fixed_rtshift" type="float" value="0.0"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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850 <param checked="true" falsevalue="" help="(-label_proteins) (select 'false' if you only need peptide-labeling)" label="Enables protein-labeling" name="param_algorithm_MSSim_Labeling_ICPL_label_proteins" optional="True" truevalue="-algorithm:MSSim:Labeling:ICPL:label_proteins" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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851 <param help="(-fixed_rtshift) If set to 0.0 only the retention times computed by the RT model step are used" label="Fixed retention time shift between labeled peptides" min="0.0" name="param_algorithm_MSSim_Labeling_SILAC_fixed_rtshift" optional="True" type="float" value="0.0001"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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852 <param help="(-modification_lysine) " label="Modification of Lysine in the medium SILAC channel" name="param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_lysine" size="30" type="text" value="UniMod:481">
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853 <sanitizer>
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854 <valid initial="string.printable">
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855 <remove value="'"/>
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856 <remove value="&quot;"/>
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857 </valid>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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858 </sanitizer>
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859 </param>
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860 <param help="(-modification_arginine) " label="Modification of Arginine in the medium SILAC channel" name="param_algorithm_MSSim_Labeling_SILAC_medium_channel_modification_arginine" size="30" type="text" value="UniMod:188">
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861 <sanitizer>
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862 <valid initial="string.printable">
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863 <remove value="'"/>
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864 <remove value="&quot;"/>
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865 </valid>
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866 </sanitizer>
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867 </param>
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868 <param help="(-modification_lysine) If left empty, two channelSILAC is assumed" label="Modification of Lysine in the heavy SILAC channel" name="param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_lysine" size="30" type="text" value="UniMod:259">
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869 <sanitizer>
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870 <valid initial="string.printable">
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871 <remove value="'"/>
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872 <remove value="&quot;"/>
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873 </valid>
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874 </sanitizer>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
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875 </param>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
876 <param help="(-modification_arginine) If left empty, two-channel SILAC is assumed" label="Modification of Arginine in the heavy SILAC channel" name="param_algorithm_MSSim_Labeling_SILAC_heavy_channel_modification_arginine" size="30" type="text" value="UniMod:267">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
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877 <sanitizer>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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878 <valid initial="string.printable">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
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879 <remove value="'"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
880 <remove value="&quot;"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
881 </valid>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
882 </sanitizer>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
883 </param>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
884 <param help="(-iTRAQ) " label="4plex or 8plex iTRAQ?" name="param_algorithm_MSSim_Labeling_itraq_iTRAQ" optional="True" type="select" value="4plex">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
885 <option value="4plex">4plex</option>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
886 <option value="8plex">8plex</option>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
887 </param>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
888 <param help="(-reporter_mass_shift) e.g. 114.1, 115.1)" label="Allowed shift (uniformly distributed - left to right) in Da from the expected position (of" max="0.5" min="0.0" name="param_algorithm_MSSim_Labeling_itraq_reporter_mass_shift" optional="True" type="float" value="0.1"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
889 <repeat max="1" min="0" name="rep_param_algorithm_MSSim_Labeling_itraq_channel_active_4plex" title="param_algorithm_MSSim_Labeling_itraq_channel_active_4plex">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
890 <param help="(-channel_active_4plex) e.g. &quot;114:myref&quot;,&quot;115:liver&quot;" 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;," name="param_algorithm_MSSim_Labeling_itraq_channel_active_4plex" size="30" type="text" value="114:myReference">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
891 <sanitizer>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
892 <valid initial="string.printable">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
893 <remove value="'"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
894 <remove value="&quot;"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
895 </valid>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
896 </sanitizer>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
897 </param>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
898 </repeat>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
899 <repeat max="1" min="0" name="rep_param_algorithm_MSSim_Labeling_itraq_channel_active_8plex" title="param_algorithm_MSSim_Labeling_itraq_channel_active_8plex">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
900 <param help="(-channel_active_8plex) e.g. &quot;113:myref&quot;,&quot;115:liver&quot;,&quot;118:lung&quot;" 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;," name="param_algorithm_MSSim_Labeling_itraq_channel_active_8plex" size="30" type="text" value="113:myReference">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
901 <sanitizer>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
902 <valid initial="string.printable">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
903 <remove value="'"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
904 <remove value="&quot;"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
905 </valid>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
906 </sanitizer>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
907 </param>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
908 </repeat>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
909 <param help="(-Y_contamination) 0=off, 1=full labeling" label="Efficiency of labeling tyrosine ('Y') residues" max="1.0" min="0.0" name="param_algorithm_MSSim_Labeling_itraq_Y_contamination" optional="True" type="float" value="0.3"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
910 <param help="(-labeling_efficiency) " label="Describes the distribution of the labeled peptide over the different states (unlabeled, mono- and di-labeled)" max="1.0" min="0.0" name="param_algorithm_MSSim_Labeling_o18_labeling_efficiency" optional="True" type="float" value="1.0"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
911 <param 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)" label="Controls the 'biological' randomness of the generated data (" name="param_algorithm_RandomNumberGenerators_biological" optional="True" type="select" value="random">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
912 <option value="reproducible">reproducible</option>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
913 <option value="random">random</option>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
914 </param>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
915 <param 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)" label="Controls the 'technical' randomness of the generated data (" name="param_algorithm_RandomNumberGenerators_technical" optional="True" type="select" value="random">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
916 <option value="reproducible">reproducible</option>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
917 <option value="random">random</option>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
918 </param>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
bgruening
parents: 0
diff changeset
919 <expand macro="advanced_options">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
920 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
921 <param 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+'" label="Maximal #combinations of charge impurities allowed (each generating one feature) per charge state" name="param_algorithm_MSSim_Ionization_esi_max_impurity_set_size" type="integer" value="3"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
922 <param help="(-ICPL_light_channel_label) " label="UniMod Id of the light channel ICPL label" name="param_algorithm_MSSim_Labeling_ICPL_ICPL_light_channel_label" size="30" type="text" value="UniMod:365">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
923 <sanitizer>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
924 <valid initial="string.printable">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
925 <remove value="'"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
926 <remove value="&quot;"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
927 </valid>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
928 </sanitizer>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
929 </param>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
930 <param help="(-ICPL_medium_channel_label) " label="UniMod Id of the medium channel ICPL label" name="param_algorithm_MSSim_Labeling_ICPL_ICPL_medium_channel_label" size="30" type="text" value="UniMod:687">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
931 <sanitizer>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
932 <valid initial="string.printable">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
933 <remove value="'"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
934 <remove value="&quot;"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
935 </valid>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
936 </sanitizer>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
937 </param>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
938 <param help="(-ICPL_heavy_channel_label) " label="UniMod Id of the heavy channel ICPL label" name="param_algorithm_MSSim_Labeling_ICPL_ICPL_heavy_channel_label" size="30" type="text" value="UniMod:364">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
939 <sanitizer>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
940 <valid initial="string.printable">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
941 <remove value="'"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
942 <remove value="&quot;"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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943 </valid>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
944 </sanitizer>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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945 </param>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
946 <repeat max="1" min="0" name="rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex" title="param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
947 <param help="(-isotope_correction_values_4plex) e.g. '114:0/0.3/4/0' , '116:0.1/0.3/3/0.2' " 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; ;" name="param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_4plex" size="30" type="text" 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">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
948 <sanitizer>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
949 <valid initial="string.printable">
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
950 <remove value="'"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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parents: 0
diff changeset
951 <remove value="&quot;"/>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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diff changeset
952 </valid>
6ead64a594bd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
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953 </sanitizer>
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954 </param>
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955 </repeat>
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956 <repeat max="1" min="0" name="rep_param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex" title="param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex">
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957 <param help="(-isotope_correction_values_8plex) e.g. '113:0/0.3/4/0' , '116:0.1/0.3/3/0.2' " 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; ;" name="param_algorithm_MSSim_Labeling_itraq_isotope_correction_values_8plex" size="30" type="text" 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">
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958 <sanitizer>
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959 <valid initial="string.printable">
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960 <remove value="'"/>
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961 <remove value="&quot;"/>
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962 </valid>
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963 </sanitizer>
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964 </param>
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965 </repeat>
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966 </expand>
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967 </inputs>
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968 <outputs>
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969 <data format="mzml" name="param_out"/>
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970 <data format="mzml" name="param_out_pm"/>
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971 <data format="xml" name="param_out_fm"/>
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972 <data format="consensusxml" name="param_out_cm"/>
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973 <data format="consensusxml" name="param_out_lcm"/>
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974 <data format="xml" name="param_out_cntm"/>
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975 <data format="xml" name="param_out_id"/>
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976 </outputs>
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977 <help>A highly configurable simulator for mass spectrometry experiments.
0
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978
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979
4
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980 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MSSimulator.html</help>
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981 </tool>