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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="PrecursorIonSelector" name="PrecursorIonSelector" version="2.0.0">
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3 <description>PrecursorIonSelector</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">PrecursorIonSelector</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>PrecursorIonSelector
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11
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12 #if $param_in:
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13 -in $param_in
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14 #end if
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15 #if $param_out:
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16 -out $param_out
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17 #end if
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18 #if $param_next_feat:
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19 -next_feat $param_next_feat
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20 #end if
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21 #if $param_ids:
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22 -ids $param_ids
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23 #end if
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24 #if $param_num_precursors:
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25 -num_precursors $param_num_precursors
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26 #end if
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27 #if $param_raw_data:
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28 -raw_data $param_raw_data
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29 #end if
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30 #if $param_load_preprocessing:
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31 -load_preprocessing
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32 #end if
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33 #if $param_store_preprocessing:
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34 -store_preprocessing
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35 #end if
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36 #if $param_simulation:
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37 -simulation
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38 #end if
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39 #if $param_sim_results:
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40 -sim_results "$param_sim_results"
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41 #end if
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42 #if $param_db_path:
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43 -db_path $param_db_path
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44 #end if
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45 #if $param_rt_model:
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46 -rt_model "$param_rt_model"
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47 #end if
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48 #if $param_dt_model:
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49 -dt_model "$param_dt_model"
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50 #end if
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51
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52 #if $rep_param_fixed_modifications:
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53 -fixed_modifications
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54 #for token in $rep_param_fixed_modifications:
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55 #if " " in str(token):
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56 "$token.param_fixed_modifications"
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57 #else
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58 $token.param_fixed_modifications
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59 #end if
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60 #end for
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61 #end if
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62 -threads \${GALAXY_SLOTS:-24}
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63 #if $param_algorithm_type:
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64 -algorithm:type
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65 #if " " in str($param_algorithm_type):
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66 "$param_algorithm_type"
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67 #else
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68 $param_algorithm_type
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69 #end if
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70 #end if
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71 #if $param_algorithm_max_iteration:
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72 -algorithm:max_iteration $param_algorithm_max_iteration
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73 #end if
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74 #if $param_algorithm_rt_bin_capacity:
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75 -algorithm:rt_bin_capacity $param_algorithm_rt_bin_capacity
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76 #end if
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77 #if $param_algorithm_step_size:
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78 -algorithm:step_size $param_algorithm_step_size
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79 #end if
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80 #if $param_algorithm_peptide_min_prob:
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81 -algorithm:peptide_min_prob $param_algorithm_peptide_min_prob
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82 #end if
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83 #if $param_algorithm_sequential_spectrum_order:
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84 -algorithm:sequential_spectrum_order
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85 #end if
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86 #if $param_algorithm_MIPFormulation_thresholds_min_protein_probability:
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87 -algorithm:MIPFormulation:thresholds:min_protein_probability $param_algorithm_MIPFormulation_thresholds_min_protein_probability
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88 #end if
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89 #if $param_algorithm_MIPFormulation_thresholds_min_protein_id_probability:
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90 -algorithm:MIPFormulation:thresholds:min_protein_id_probability $param_algorithm_MIPFormulation_thresholds_min_protein_id_probability
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91 #end if
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92 #if $param_algorithm_MIPFormulation_thresholds_min_pt_weight:
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93 -algorithm:MIPFormulation:thresholds:min_pt_weight $param_algorithm_MIPFormulation_thresholds_min_pt_weight
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94 #end if
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95 #if $param_algorithm_MIPFormulation_thresholds_min_mz:
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96 -algorithm:MIPFormulation:thresholds:min_mz $param_algorithm_MIPFormulation_thresholds_min_mz
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97 #end if
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98 #if $param_algorithm_MIPFormulation_thresholds_max_mz:
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99 -algorithm:MIPFormulation:thresholds:max_mz $param_algorithm_MIPFormulation_thresholds_max_mz
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100 #end if
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101 #if $param_algorithm_MIPFormulation_thresholds_min_pred_pep_prob:
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102 -algorithm:MIPFormulation:thresholds:min_pred_pep_prob $param_algorithm_MIPFormulation_thresholds_min_pred_pep_prob
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103 #end if
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104 #if $param_algorithm_MIPFormulation_thresholds_min_rt_weight:
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105 -algorithm:MIPFormulation:thresholds:min_rt_weight $param_algorithm_MIPFormulation_thresholds_min_rt_weight
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106 #end if
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107 #if $param_algorithm_MIPFormulation_thresholds_use_peptide_rule:
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108 -algorithm:MIPFormulation:thresholds:use_peptide_rule
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109 #end if
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110 #if $param_algorithm_MIPFormulation_thresholds_min_peptide_ids:
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111 -algorithm:MIPFormulation:thresholds:min_peptide_ids $param_algorithm_MIPFormulation_thresholds_min_peptide_ids
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112 #end if
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113 #if $param_algorithm_MIPFormulation_thresholds_min_peptide_probability:
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114 -algorithm:MIPFormulation:thresholds:min_peptide_probability $param_algorithm_MIPFormulation_thresholds_min_peptide_probability
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115 #end if
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116 #if $param_algorithm_MIPFormulation_combined_ilp_k1:
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117 -algorithm:MIPFormulation:combined_ilp:k1 $param_algorithm_MIPFormulation_combined_ilp_k1
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118 #end if
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119 #if $param_algorithm_MIPFormulation_combined_ilp_k2:
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120 -algorithm:MIPFormulation:combined_ilp:k2 $param_algorithm_MIPFormulation_combined_ilp_k2
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121 #end if
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122 #if $param_algorithm_MIPFormulation_combined_ilp_k3:
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123 -algorithm:MIPFormulation:combined_ilp:k3 $param_algorithm_MIPFormulation_combined_ilp_k3
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124 #end if
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125 #if $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs:
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126 -algorithm:MIPFormulation:combined_ilp:scale_matching_probs
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127 #end if
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128 #if $param_algorithm_MIPFormulation_feature_based_no_intensity_normalization:
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129 -algorithm:MIPFormulation:feature_based:no_intensity_normalization
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130 #end if
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131 #if $param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature:
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132 -algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature $param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature
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133 #end if
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134 #if $param_algorithm_Preprocessing_precursor_mass_tolerance:
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135 -algorithm:Preprocessing:precursor_mass_tolerance $param_algorithm_Preprocessing_precursor_mass_tolerance
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136 #end if
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137 #if $param_algorithm_Preprocessing_precursor_mass_tolerance_unit:
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138 -algorithm:Preprocessing:precursor_mass_tolerance_unit
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139 #if " " in str($param_algorithm_Preprocessing_precursor_mass_tolerance_unit):
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140 "$param_algorithm_Preprocessing_precursor_mass_tolerance_unit"
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141 #else
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142 $param_algorithm_Preprocessing_precursor_mass_tolerance_unit
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143 #end if
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144 #end if
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145 #if $param_algorithm_Preprocessing_preprocessed_db_path:
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146 -algorithm:Preprocessing:preprocessed_db_path "$param_algorithm_Preprocessing_preprocessed_db_path"
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147 #end if
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148 #if $param_algorithm_Preprocessing_preprocessed_db_pred_rt_path:
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149 -algorithm:Preprocessing:preprocessed_db_pred_rt_path "$param_algorithm_Preprocessing_preprocessed_db_pred_rt_path"
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150 #end if
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151 #if $param_algorithm_Preprocessing_preprocessed_db_pred_dt_path:
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152 -algorithm:Preprocessing:preprocessed_db_pred_dt_path "$param_algorithm_Preprocessing_preprocessed_db_pred_dt_path"
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153 #end if
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154 #if $param_algorithm_Preprocessing_max_peptides_per_run:
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155 -algorithm:Preprocessing:max_peptides_per_run $param_algorithm_Preprocessing_max_peptides_per_run
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156 #end if
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157 #if $param_algorithm_Preprocessing_missed_cleavages:
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158 -algorithm:Preprocessing:missed_cleavages $param_algorithm_Preprocessing_missed_cleavages
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159 #end if
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160 #if $param_algorithm_Preprocessing_taxonomy:
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161 -algorithm:Preprocessing:taxonomy "$param_algorithm_Preprocessing_taxonomy"
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162 #end if
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163 #if $param_algorithm_Preprocessing_tmp_dir:
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164 -algorithm:Preprocessing:tmp_dir "$param_algorithm_Preprocessing_tmp_dir"
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165 #end if
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166 #if $param_algorithm_Preprocessing_store_peptide_sequences:
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167 -algorithm:Preprocessing:store_peptide_sequences "$param_algorithm_Preprocessing_store_peptide_sequences"
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168 #end if
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169 #if $param_algorithm_Preprocessing_rt_settings_min_rt:
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170 -algorithm:Preprocessing:rt_settings:min_rt $param_algorithm_Preprocessing_rt_settings_min_rt
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171 #end if
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172 #if $param_algorithm_Preprocessing_rt_settings_max_rt:
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173 -algorithm:Preprocessing:rt_settings:max_rt $param_algorithm_Preprocessing_rt_settings_max_rt
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174 #end if
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175 #if $param_algorithm_Preprocessing_rt_settings_rt_step_size:
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176 -algorithm:Preprocessing:rt_settings:rt_step_size $param_algorithm_Preprocessing_rt_settings_rt_step_size
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177 #end if
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178 #if $param_algorithm_Preprocessing_rt_settings_gauss_mean:
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179 -algorithm:Preprocessing:rt_settings:gauss_mean $param_algorithm_Preprocessing_rt_settings_gauss_mean
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180 #end if
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181 #if $param_algorithm_Preprocessing_rt_settings_gauss_sigma:
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182 -algorithm:Preprocessing:rt_settings:gauss_sigma $param_algorithm_Preprocessing_rt_settings_gauss_sigma
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183 #end if
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184 #if $adv_opts.adv_opts_selector=='advanced':
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185 #if $adv_opts.param_solver:
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186 -solver
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187 #if " " in str($adv_opts.param_solver):
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188 "$adv_opts.param_solver"
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189 #else
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190 $adv_opts.param_solver
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191 #end if
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192 #end if
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193 #if $adv_opts.param_force:
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194 -force
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195 #end if
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196 #end if
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197 </command>
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198 <inputs>
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199 <param name="param_in" type="data" format="featurexml" optional="False" label="Input feature map file (featureXML)" help="(-in) "/>
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200 <param name="param_ids" type="data" format="idxml" optional="False" label="file containing results of identification" help="(-ids) "/>
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201 <param name="param_num_precursors" type="integer" value="1" label="number of precursors to be selected" help="(-num_precursors) "/>
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202 <param name="param_raw_data" type="data" format="mzml" optional="True" label="Input profile data" help="(-raw_data) "/>
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203 <param name="param_load_preprocessing" type="boolean" truevalue="-load_preprocessing" falsevalue="" checked="false" optional="True" label="The preprocessed db is loaded from file, not calculated" help="(-load_preprocessing) "/>
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204 <param name="param_store_preprocessing" type="boolean" truevalue="-store_preprocessing" falsevalue="" checked="false" optional="True" label="The preprocessed db is stored" help="(-store_preprocessing) "/>
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205 <param name="param_simulation" type="boolean" truevalue="-simulation" falsevalue="" checked="false" optional="True" label="Simulate the whole LC-MS/MS run" help="(-simulation) "/>
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206 <param name="param_sim_results" type="text" size="30" label="File containing the results of the simulation run" help="(-sim_results) ">
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207 <sanitizer>
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208 <valid initial="string.printable">
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209 <remove value="'"/>
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210 <remove value="""/>
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211 </valid>
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212 </sanitizer>
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213 </param>
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214 <param name="param_db_path" type="data" format="fasta" optional="True" label="db file" help="(-db_path) "/>
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215 <param name="param_rt_model" type="text" size="30" label="SVM Model for RTPredict" help="(-rt_model) ">
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216 <sanitizer>
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217 <valid initial="string.printable">
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218 <remove value="'"/>
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219 <remove value="""/>
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220 </valid>
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221 </sanitizer>
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222 </param>
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223 <param name="param_dt_model" type="text" size="30" label="SVM Model for PTPredict" help="(-dt_model) ">
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224 <sanitizer>
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225 <valid initial="string.printable">
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226 <remove value="'"/>
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227 <remove value="""/>
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228 </valid>
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229 </sanitizer>
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230 </param>
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231 <repeat name="rep_param_fixed_modifications" min="0" title="param_fixed_modifications">
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232 <param name="param_fixed_modifications" type="text" size="30" label="the modifications i.e. Carboxymethyl (C)" help="(-fixed_modifications) ">
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233 <sanitizer>
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234 <valid initial="string.printable">
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235 <remove value="'"/>
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236 <remove value="""/>
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237 </valid>
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238 </sanitizer>
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239 </param>
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240 </repeat>
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241 <param name="param_algorithm_type" type="select" optional="True" value="IPS" label="Strategy for precursor ion selection" help="(-type) ">
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242 <option value="ILP_IPS">ILP_IPS</option>
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243 <option value="IPS">IPS</option>
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244 <option value="SPS">SPS</option>
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245 <option value="Upshift">Upshift</option>
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246 <option value="Downshift">Downshift</option>
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247 <option value="DEX">DEX</option>
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248 </param>
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249 <param name="param_algorithm_max_iteration" type="integer" min="1" optional="True" value="100" label="Maximal number of iterations" help="(-max_iteration) "/>
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250 <param name="param_algorithm_rt_bin_capacity" type="integer" min="1" optional="True" value="10" label="Maximal number of precursors per rt bin" help="(-rt_bin_capacity) "/>
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251 <param name="param_algorithm_step_size" type="integer" min="1" optional="True" value="1" label="Maximal number of precursors per iteration" help="(-step_size) "/>
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252 <param name="param_algorithm_peptide_min_prob" type="float" value="0.2" label="Minimal peptide probability" help="(-peptide_min_prob) "/>
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253 <param name="param_algorithm_sequential_spectrum_order" type="boolean" truevalue="-algorithm:sequential_spectrum_order" falsevalue="" checked="false" optional="True" label="If true, precursors are selected sequentially with respect to their RT" help="(-sequential_spectrum_order) "/>
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254 <param name="param_algorithm_MIPFormulation_thresholds_min_protein_probability" type="float" min="0.0" max="1.0" optional="True" value="0.2" label="Minimal protein probability for a protein to be considered in the ILP" help="(-min_protein_probability) "/>
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255 <param name="param_algorithm_MIPFormulation_thresholds_min_protein_id_probability" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="Minimal protein probability for a protein to be considered identified" help="(-min_protein_id_probability) "/>
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256 <param name="param_algorithm_MIPFormulation_thresholds_min_pt_weight" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal pt weight of a precurso" help="(-min_pt_weight) "/>
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257 <param name="param_algorithm_MIPFormulation_thresholds_min_mz" type="float" min="0.0" optional="True" value="500.0" label="Minimal mz to be considered in protein based LP formulation" help="(-min_mz) "/>
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258 <param name="param_algorithm_MIPFormulation_thresholds_max_mz" type="float" min="0.0" optional="True" value="5000.0" label="Minimal mz to be considered in protein based LP formulation" help="(-max_mz) "/>
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259 <param name="param_algorithm_MIPFormulation_thresholds_min_pred_pep_prob" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal predicted peptide probability of a precurso" help="(-min_pred_pep_prob) "/>
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260 <param name="param_algorithm_MIPFormulation_thresholds_min_rt_weight" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal rt weight of a precurso" help="(-min_rt_weight) "/>
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261 <param name="param_algorithm_MIPFormulation_thresholds_use_peptide_rule" type="boolean" truevalue="-algorithm:MIPFormulation:thresholds:use_peptide_rule" falsevalue="" checked="false" optional="True" label="Use peptide rule instead of minimal protein id probability" help="(-use_peptide_rule) "/>
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262 <param name="param_algorithm_MIPFormulation_thresholds_min_peptide_ids" type="integer" min="1" optional="True" value="2" label="If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id" help="(-min_peptide_ids) "/>
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263 <param name="param_algorithm_MIPFormulation_thresholds_min_peptide_probability" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified" help="(-min_peptide_probability) "/>
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264 <param name="param_algorithm_MIPFormulation_combined_ilp_k1" type="float" min="0.0" optional="True" value="0.2" label="combined ilp: weight for z_i" help="(-k1) "/>
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265 <param name="param_algorithm_MIPFormulation_combined_ilp_k2" type="float" min="0.0" optional="True" value="0.2" label="combined ilp: weight for x_j,s*int_j,s" help="(-k2) "/>
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266 <param name="param_algorithm_MIPFormulation_combined_ilp_k3" type="float" min="0.0" optional="True" value="0.4" label="combined ilp: weight for -x_j,s*w_j,s" help="(-k3) "/>
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267 <param name="param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs" type="boolean" truevalue="-algorithm:MIPFormulation:combined_ilp:scale_matching_probs" falsevalue="" checked="true" optional="True" label="flag if detectability * rt_weight shall be scaled to cover all [0,1]" help="(-scale_matching_probs) "/>
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268 <param name="param_algorithm_MIPFormulation_feature_based_no_intensity_normalization" type="boolean" truevalue="-algorithm:MIPFormulation:feature_based:no_intensity_normalization" falsevalue="" checked="false" optional="True" label="Flag indicating if intensities shall be scaled to be in [0,1]" help="(-no_intensity_normalization) This is done for each feature separately, so that the feature's maximal intensity in a spectrum is set to 1"/>
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269 <param name="param_algorithm_MIPFormulation_feature_based_max_number_precursors_per_feature" type="integer" min="1" optional="True" value="1" label="The maximal number of precursors per feature" help="(-max_number_precursors_per_feature) "/>
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270 <param name="param_algorithm_Preprocessing_precursor_mass_tolerance" type="float" min="0.0" optional="True" value="10.0" label="Precursor mass tolerance which is used to query the peptide database for peptides" help="(-precursor_mass_tolerance) "/>
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271 <param name="param_algorithm_Preprocessing_precursor_mass_tolerance_unit" type="select" optional="True" value="ppm" label="Precursor mass tolerance unit" help="(-precursor_mass_tolerance_unit) ">
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272 <option value="ppm">ppm</option>
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273 <option value="Da">Da</option>
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274 </param>
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275 <param name="param_algorithm_Preprocessing_preprocessed_db_path" type="text" size="30" label="Path where the preprocessed database should be stored" help="(-preprocessed_db_path) ">
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276 <sanitizer>
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277 <valid initial="string.printable">
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278 <remove value="'"/>
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279 <remove value="""/>
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280 </valid>
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281 </sanitizer>
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282 </param>
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283 <param name="param_algorithm_Preprocessing_preprocessed_db_pred_rt_path" type="text" size="30" label="Path where the predicted rts of the preprocessed database should be stored" help="(-preprocessed_db_pred_rt_path) ">
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284 <sanitizer>
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285 <valid initial="string.printable">
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286 <remove value="'"/>
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287 <remove value="""/>
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288 </valid>
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289 </sanitizer>
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290 </param>
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291 <param name="param_algorithm_Preprocessing_preprocessed_db_pred_dt_path" type="text" size="30" label="Path where the predicted rts of the preprocessed database should be stored" help="(-preprocessed_db_pred_dt_path) ">
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292 <sanitizer>
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293 <valid initial="string.printable">
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294 <remove value="'"/>
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295 <remove value="""/>
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296 </valid>
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297 </sanitizer>
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298 </param>
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299 <param name="param_algorithm_Preprocessing_max_peptides_per_run" type="integer" min="1" optional="True" value="100000" label="Number of peptides for that the pt and rt are parallely predicted" help="(-max_peptides_per_run) "/>
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300 <param name="param_algorithm_Preprocessing_missed_cleavages" type="integer" min="0" optional="True" value="1" label="Number of allowed missed cleavages" help="(-missed_cleavages) "/>
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301 <param name="param_algorithm_Preprocessing_taxonomy" type="text" size="30" label="Taxonomy" help="(-taxonomy) ">
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302 <sanitizer>
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303 <valid initial="string.printable">
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304 <remove value="'"/>
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305 <remove value="""/>
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306 </valid>
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307 </sanitizer>
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308 </param>
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309 <param name="param_algorithm_Preprocessing_tmp_dir" type="text" size="30" label="Absolute path to tmp data directory used to store files needed for rt and dt prediction" help="(-tmp_dir) ">
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310 <sanitizer>
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311 <valid initial="string.printable">
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312 <remove value="'"/>
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313 <remove value="""/>
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314 </valid>
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315 </sanitizer>
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316 </param>
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317 <param name="param_algorithm_Preprocessing_store_peptide_sequences" type="text" size="30" value="false" label="Flag if peptide sequences should be stored" help="(-store_peptide_sequences) ">
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318 <sanitizer>
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319 <valid initial="string.printable">
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320 <remove value="'"/>
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321 <remove value="""/>
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322 </valid>
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323 </sanitizer>
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324 </param>
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325 <param name="param_algorithm_Preprocessing_rt_settings_min_rt" type="float" min="1.0" optional="True" value="960.0" label="Minimal RT in the experiment (in seconds)" help="(-min_rt) "/>
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326 <param name="param_algorithm_Preprocessing_rt_settings_max_rt" type="float" value="3840.0" label="Maximal RT in the experiment (in seconds)" help="(-max_rt) "/>
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327 <param name="param_algorithm_Preprocessing_rt_settings_rt_step_size" type="float" value="30.0" label="Time between two consecutive spectra (in seconds)" help="(-rt_step_size) "/>
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328 <param name="param_algorithm_Preprocessing_rt_settings_gauss_mean" type="float" value="-1.0" label="mean of the gauss curve" help="(-gauss_mean) "/>
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329 <param name="param_algorithm_Preprocessing_rt_settings_gauss_sigma" type="float" value="3.0" label="std of the gauss curve" help="(-gauss_sigma) "/>
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330 <expand macro="advanced_options">
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331 <param name="param_solver" type="select" optional="True" value="GLPK" label="LP solver type" help="(-solver) ">
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332 <option value="GLPK">GLPK</option>
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333 <option value="COINOR">COINOR</option>
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334 </param>
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335 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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336 </expand>
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337 </inputs>
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338 <outputs>
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339 <data name="param_out" format="featurexml"/>
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340 <data name="param_next_feat" format="featurexml"/>
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341 </outputs>
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342 <help>**What it does**
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343
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344 PrecursorIonSelector
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345
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346
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347 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_PrecursorIonSelector.html</help>
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348 <expand macro="references"/>
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349 </tool>
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