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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="InclusionExclusionListCreator" name="InclusionExclusionListCreator" version="2.0.0">
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3 <description>Creates inclusion and/or exclusion lists.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">InclusionExclusionListCreator</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>InclusionExclusionListCreator
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11
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12 #if $param_include:
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13 -include $param_include
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14 #end if
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15 #if $param_exclude:
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16 -exclude $param_exclude
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 #if $param_rt_model:
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22 -rt_model $param_rt_model
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23 #end if
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24 #if $param_pt_model:
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25 -pt_model $param_pt_model
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26 #end if
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27
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28 #if $rep_param_inclusion_charges:
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29 -inclusion_charges
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30 #for token in $rep_param_inclusion_charges:
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31 #if " " in str(token):
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32 "$token.param_inclusion_charges"
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33 #else
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34 $token.param_inclusion_charges
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35 #end if
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36 #end for
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37 #end if
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38 #if $param_inclusion_strategy:
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39 -inclusion_strategy
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40 #if " " in str($param_inclusion_strategy):
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41 "$param_inclusion_strategy"
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42 #else
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43 $param_inclusion_strategy
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44 #end if
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45 #end if
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46
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47 #if $rep_param_exclusion_charges:
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48 -exclusion_charges
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49 #for token in $rep_param_exclusion_charges:
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50 #if " " in str(token):
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51 "$token.param_exclusion_charges"
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52 #else
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53 $token.param_exclusion_charges
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54 #end if
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55 #end for
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56 #end if
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57 #if $param_raw_data:
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58 -raw_data $param_raw_data
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59 #end if
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60 -threads \${GALAXY_SLOTS:-24}
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61 #if $param_algorithm_InclusionExclusionList_missed_cleavages:
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62 -algorithm:InclusionExclusionList:missed_cleavages $param_algorithm_InclusionExclusionList_missed_cleavages
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63 #end if
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64 #if $param_algorithm_InclusionExclusionList_RT_unit:
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65 -algorithm:InclusionExclusionList:RT:unit
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66 #if " " in str($param_algorithm_InclusionExclusionList_RT_unit):
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67 "$param_algorithm_InclusionExclusionList_RT_unit"
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68 #else
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69 $param_algorithm_InclusionExclusionList_RT_unit
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70 #end if
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71 #end if
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72 #if $param_algorithm_InclusionExclusionList_RT_use_relative:
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73 -algorithm:InclusionExclusionList:RT:use_relative
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74 #end if
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75 #if $param_algorithm_InclusionExclusionList_RT_window_relative:
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76 -algorithm:InclusionExclusionList:RT:window_relative $param_algorithm_InclusionExclusionList_RT_window_relative
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77 #end if
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78 #if $param_algorithm_InclusionExclusionList_RT_window_absolute:
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79 -algorithm:InclusionExclusionList:RT:window_absolute $param_algorithm_InclusionExclusionList_RT_window_absolute
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80 #end if
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81 #if $param_algorithm_InclusionExclusionList_merge_mz_tol:
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82 -algorithm:InclusionExclusionList:merge:mz_tol $param_algorithm_InclusionExclusionList_merge_mz_tol
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83 #end if
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84 #if $param_algorithm_InclusionExclusionList_merge_mz_tol_unit:
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85 -algorithm:InclusionExclusionList:merge:mz_tol_unit
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86 #if " " in str($param_algorithm_InclusionExclusionList_merge_mz_tol_unit):
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87 "$param_algorithm_InclusionExclusionList_merge_mz_tol_unit"
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88 #else
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89 $param_algorithm_InclusionExclusionList_merge_mz_tol_unit
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90 #end if
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91 #end if
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92 #if $param_algorithm_InclusionExclusionList_merge_rt_tol:
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93 -algorithm:InclusionExclusionList:merge:rt_tol $param_algorithm_InclusionExclusionList_merge_rt_tol
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94 #end if
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95 #if $param_algorithm_PrecursorSelection_ms2_spectra_per_rt_bin:
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96 -algorithm:PrecursorSelection:ms2_spectra_per_rt_bin $param_algorithm_PrecursorSelection_ms2_spectra_per_rt_bin
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97 #end if
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98 #if $param_algorithm_PrecursorSelection_exclude_overlapping_peaks:
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99 -algorithm:PrecursorSelection:exclude_overlapping_peaks
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100 #end if
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101 #if $param_algorithm_PrecursorSelection_Exclusion_use_dynamic_exclusion:
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102 -algorithm:PrecursorSelection:Exclusion:use_dynamic_exclusion
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103 #end if
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104 #if $param_algorithm_PrecursorSelection_Exclusion_exclusion_time:
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105 -algorithm:PrecursorSelection:Exclusion:exclusion_time $param_algorithm_PrecursorSelection_Exclusion_exclusion_time
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106 #end if
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107 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_max_list_size:
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108 -algorithm:PrecursorSelection:ProteinBasedInclusion:max_list_size $param_algorithm_PrecursorSelection_ProteinBasedInclusion_max_list_size
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109 #end if
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110 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_min_rt:
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111 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:min_rt $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_min_rt
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112 #end if
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113 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_max_rt:
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114 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:max_rt $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_max_rt
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115 #end if
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116 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_step_size:
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117 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_step_size $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_step_size
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118 #end if
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119 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_window_size:
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120 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_window_size $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_window_size
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121 #end if
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122 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_protein_id_probability:
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123 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_protein_id_probability $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_protein_id_probability
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124 #end if
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125 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_pt_weight:
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126 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_pt_weight $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_pt_weight
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127 #end if
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128 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_mz:
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129 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_mz $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_mz
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130 #end if
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131 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_max_mz:
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132 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:max_mz $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_max_mz
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133 #end if
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134 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_use_peptide_rule:
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135 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:use_peptide_rule
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136 #end if
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137 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_ids:
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138 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_ids $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_ids
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139 #end if
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140 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_probability:
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141 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_probability $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_probability
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142 #end if
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143 #if $param_algorithm_PrecursorSelection_feature_based_no_intensity_normalization:
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144 -algorithm:PrecursorSelection:feature_based:no_intensity_normalization
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145 #end if
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146 #if $param_algorithm_PrecursorSelection_feature_based_max_number_precursors_per_feature:
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147 -algorithm:PrecursorSelection:feature_based:max_number_precursors_per_feature $param_algorithm_PrecursorSelection_feature_based_max_number_precursors_per_feature
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148 #end if
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149 #if $adv_opts.adv_opts_selector=='advanced':
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150 #if $adv_opts.param_force:
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151 -force
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152 #end if
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153 #end if
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154 </command>
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155 <inputs>
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156 <param name="param_include" type="data" format="fasta,featurexml" optional="True" label="Inclusion list input file in FASTA or featureXML format" help="(-include) "/>
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157 <param name="param_exclude" type="data" format="fasta,featurexml,idxml" optional="True" label="Exclusion list input file in featureXML, idXML or FASTA format" help="(-exclude) "/>
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158 <param name="param_rt_model" type="data" format="txt" optional="True" label="RTModel file used for the rt prediction of peptides in FASTA files" help="(-rt_model) "/>
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159 <param name="param_pt_model" type="data" format="txt" optional="True" label="PTModel file used for the pt prediction of peptides in FASTA files (only needed for inclusion_strategy PreotinBased_LP)" help="(-pt_model) "/>
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160 <repeat name="rep_param_inclusion_charges" min="0" title="param_inclusion_charges">
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161 <param name="param_inclusion_charges" type="text" min="1" optional="True" size="30" value="1" label="List containing the charge states to be considered for the inclusion list compounds, space separated" help="(-inclusion_charges) ">
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162 <sanitizer>
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163 <valid initial="string.printable">
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164 <remove value="'"/>
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165 <remove value="""/>
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166 </valid>
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167 </sanitizer>
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168 </param>
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169 </repeat>
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170 <param name="param_inclusion_strategy" type="select" optional="True" value="ALL" label="strategy to be used for selection" help="(-inclusion_strategy) ">
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171 <option value="FeatureBased_LP">FeatureBased_LP</option>
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172 <option value="ProteinBased_LP">ProteinBased_LP</option>
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173 <option value="ALL">ALL</option>
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174 </param>
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175 <repeat name="rep_param_exclusion_charges" min="0" title="param_exclusion_charges">
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176 <param name="param_exclusion_charges" type="text" min="1" optional="True" size="30" value="1" label="List containing the charge states to be considered for the exclusion list compounds (for idXML and FASTA input), space separated" help="(-exclusion_charges) ">
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177 <sanitizer>
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178 <valid initial="string.printable">
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179 <remove value="'"/>
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180 <remove value="""/>
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181 </valid>
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182 </sanitizer>
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183 </param>
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184 </repeat>
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185 <param name="param_raw_data" type="data" format="mzml" optional="True" label="File containing the raw data (only needed for FeatureBased_LP)" help="(-raw_data) "/>
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186 <param name="param_algorithm_InclusionExclusionList_missed_cleavages" type="integer" value="0" label="Number of missed cleavages used for protein digestion" help="(-missed_cleavages) <br>"/>
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187 <param name="param_algorithm_InclusionExclusionList_RT_unit" type="select" optional="True" value="minutes" label="Create lists with units as seconds instead of minutes" help="(-unit) ">
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188 <option value="minutes">minutes</option>
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189 <option value="seconds">seconds</option>
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190 </param>
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191 <param name="param_algorithm_InclusionExclusionList_RT_use_relative" type="boolean" truevalue="-algorithm:InclusionExclusionList:RT:use_relative" falsevalue="" checked="true" optional="True" label="Use relative RT window, which depends on RT of precurso" help="(-use_relative) "/>
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192 <param name="param_algorithm_InclusionExclusionList_RT_window_relative" type="float" min="0.0" max="10.0" optional="True" value="0.05" label="[for RT:use_relative == true] The relative factor X for the RT exclusion window," help="(-window_relative) e.g. the window is calculated as [rt - rt*X, rt + rt*X]"/>
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193 <param name="param_algorithm_InclusionExclusionList_RT_window_absolute" type="float" min="0.0" optional="True" value="90.0" label="[for RT:use_relative == false] The absolute value X for the RT exclusion window in [sec]," help="(-window_absolute) e.g. the window is calculated as [rt - X, rt + X]"/>
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194 <param name="param_algorithm_InclusionExclusionList_merge_mz_tol" type="float" min="0.0" optional="True" value="10.0" label="Two inclusion/exclusion windows are merged when they (almost) overlap in RT (see 'rt_tol') and are close in m/z by this tolerance" help="(-mz_tol) Unit of this is defined in 'mz_tol_unit'"/>
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195 <param name="param_algorithm_InclusionExclusionList_merge_mz_tol_unit" type="select" optional="True" value="ppm" label="Unit of 'mz_tol'" help="(-mz_tol_unit) ">
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196 <option value="ppm">ppm</option>
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197 <option value="Da">Da</option>
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198 </param>
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199 <param name="param_algorithm_InclusionExclusionList_merge_rt_tol" type="float" min="0.0" optional="True" value="1.1" label="Maximal RT delta (in seconds) which would allow two windows in RT to overlap (which causes merging the windows)" help="(-rt_tol) Two inclusion/exclusion windows are merged when they (almost) overlap in RT and are close in m/z by this tolerance (see 'mz_tol'). Unit of this param is [seconds]"/>
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200 <param name="param_algorithm_PrecursorSelection_ms2_spectra_per_rt_bin" type="integer" min="1" optional="True" value="5" label="Number of allowed MS/MS spectra in a retention time bin" help="(-ms2_spectra_per_rt_bin) "/>
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201 <param name="param_algorithm_PrecursorSelection_exclude_overlapping_peaks" type="boolean" truevalue="-algorithm:PrecursorSelection:exclude_overlapping_peaks" falsevalue="" checked="false" optional="True" label="If true overlapping or nearby peaks (within min_peak_distance) are excluded for selection" help="(-exclude_overlapping_peaks) "/>
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202 <param name="param_algorithm_PrecursorSelection_Exclusion_use_dynamic_exclusion" type="boolean" truevalue="-algorithm:PrecursorSelection:Exclusion:use_dynamic_exclusion" falsevalue="" checked="false" optional="True" label="If true dynamic exclusion is applied" help="(-use_dynamic_exclusion) "/>
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203 <param name="param_algorithm_PrecursorSelection_Exclusion_exclusion_time" type="float" min="0.0" optional="True" value="100.0" label="The time (in seconds) a feature is excluded" help="(-exclusion_time) "/>
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204 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_max_list_size" type="integer" min="1" optional="True" value="1000" label="The maximal number of precursors in the inclusion list" help="(-max_list_size) "/>
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205 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_min_rt" type="float" min="0.0" optional="True" value="960.0" label="Minimal rt in seconds" help="(-min_rt) "/>
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206 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_max_rt" type="float" min="0.0" optional="True" value="3840.0" label="Maximal rt in seconds" help="(-max_rt) "/>
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207 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_step_size" type="float" min="1.0" optional="True" value="30.0" label="rt step size in seconds" help="(-rt_step_size) "/>
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208 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_window_size" type="integer" min="1" optional="True" value="100" label="rt window size in seconds" help="(-rt_window_size) "/>
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209 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_protein_id_probability" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="Minimal protein probability for a protein to be considered identified" help="(-min_protein_id_probability) "/>
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210 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_pt_weight" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Minimal pt weight of a precurso" help="(-min_pt_weight) "/>
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211 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_mz" type="float" min="0.0" optional="True" value="500.0" label="Minimal mz to be considered in protein based LP formulation" help="(-min_mz) "/>
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212 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_max_mz" type="float" min="0.0" optional="True" value="5000.0" label="Minimal mz to be considered in protein based LP formulation" help="(-max_mz) "/>
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213 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_use_peptide_rule" type="boolean" truevalue="-algorithm:PrecursorSelection:ProteinBasedInclusion: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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214 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_ids" type="integer" min="1" optional="True" value="2" label="If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id" help="(-min_peptide_ids) "/>
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215 <param name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_probability" type="float" min="0.0" max="1.0" optional="True" value="0.95" label="If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified" help="(-min_peptide_probability) "/>
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216 <param name="param_algorithm_PrecursorSelection_feature_based_no_intensity_normalization" type="boolean" truevalue="-algorithm:PrecursorSelection: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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217 <param name="param_algorithm_PrecursorSelection_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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218 <expand macro="advanced_options">
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219 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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220 </expand>
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221 </inputs>
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222 <outputs>
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223 <data name="param_out" format="tabular"/>
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224 </outputs>
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225 <help>**What it does**
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226
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227 Creates inclusion and/or exclusion lists.
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228
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229
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230 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InclusionExclusionListCreator.html</help>
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231 <expand macro="references"/>
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232 </tool>
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