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

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author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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4
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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: [Targeted Experiments]-->
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4 <tool id="InclusionExclusionListCreator" name="InclusionExclusionListCreator" version="2.0.0">
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5 <description>Creates inclusion and/or exclusion lists.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">InclusionExclusionListCreator</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>InclusionExclusionListCreator
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14
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15 #if $param_include:
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16 -include $param_include
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17 #end if
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18 #if $param_exclude:
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19 -exclude $param_exclude
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20 #end if
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21 #if $param_out:
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22 -out $param_out
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23 #end if
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24 #if $param_rt_model:
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25 -rt_model $param_rt_model
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26 #end if
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27 #if $param_pt_model:
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28 -pt_model $param_pt_model
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29 #end if
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30
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31 #if $rep_param_inclusion_charges:
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32 -inclusion_charges
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33 #for token in $rep_param_inclusion_charges:
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34 #if &quot; &quot; in str(token):
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35 &quot;$token.param_inclusion_charges&quot;
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36 #else
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37 $token.param_inclusion_charges
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38 #end if
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39 #end for
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40 #end if
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41 #if $param_inclusion_strategy:
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42 -inclusion_strategy
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43 #if &quot; &quot; in str($param_inclusion_strategy):
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44 &quot;$param_inclusion_strategy&quot;
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45 #else
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46 $param_inclusion_strategy
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47 #end if
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48 #end if
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49
4
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50 #if $rep_param_exclusion_charges:
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51 -exclusion_charges
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52 #for token in $rep_param_exclusion_charges:
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53 #if &quot; &quot; in str(token):
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54 &quot;$token.param_exclusion_charges&quot;
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55 #else
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56 $token.param_exclusion_charges
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57 #end if
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58 #end for
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59 #end if
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60 #if $param_raw_data:
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61 -raw_data $param_raw_data
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62 #end if
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63 -threads \${GALAXY_SLOTS:-24}
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64 #if $param_algorithm_InclusionExclusionList_missed_cleavages:
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65 -algorithm:InclusionExclusionList:missed_cleavages $param_algorithm_InclusionExclusionList_missed_cleavages
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66 #end if
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67 #if $param_algorithm_InclusionExclusionList_RT_unit:
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68 -algorithm:InclusionExclusionList:RT:unit
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69 #if &quot; &quot; in str($param_algorithm_InclusionExclusionList_RT_unit):
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70 &quot;$param_algorithm_InclusionExclusionList_RT_unit&quot;
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71 #else
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72 $param_algorithm_InclusionExclusionList_RT_unit
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73 #end if
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74 #end if
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75 #if $param_algorithm_InclusionExclusionList_RT_use_relative:
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76 -algorithm:InclusionExclusionList:RT:use_relative
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77 #end if
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78 #if $param_algorithm_InclusionExclusionList_RT_window_relative:
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79 -algorithm:InclusionExclusionList:RT:window_relative $param_algorithm_InclusionExclusionList_RT_window_relative
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80 #end if
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81 #if $param_algorithm_InclusionExclusionList_RT_window_absolute:
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82 -algorithm:InclusionExclusionList:RT:window_absolute $param_algorithm_InclusionExclusionList_RT_window_absolute
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83 #end if
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84 #if $param_algorithm_InclusionExclusionList_merge_mz_tol:
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85 -algorithm:InclusionExclusionList:merge:mz_tol $param_algorithm_InclusionExclusionList_merge_mz_tol
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86 #end if
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87 #if $param_algorithm_InclusionExclusionList_merge_mz_tol_unit:
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88 -algorithm:InclusionExclusionList:merge:mz_tol_unit
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89 #if &quot; &quot; in str($param_algorithm_InclusionExclusionList_merge_mz_tol_unit):
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90 &quot;$param_algorithm_InclusionExclusionList_merge_mz_tol_unit&quot;
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91 #else
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92 $param_algorithm_InclusionExclusionList_merge_mz_tol_unit
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93 #end if
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94 #end if
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95 #if $param_algorithm_InclusionExclusionList_merge_rt_tol:
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96 -algorithm:InclusionExclusionList:merge:rt_tol $param_algorithm_InclusionExclusionList_merge_rt_tol
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97 #end if
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98 #if $param_algorithm_PrecursorSelection_ms2_spectra_per_rt_bin:
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99 -algorithm:PrecursorSelection:ms2_spectra_per_rt_bin $param_algorithm_PrecursorSelection_ms2_spectra_per_rt_bin
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100 #end if
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101 #if $param_algorithm_PrecursorSelection_exclude_overlapping_peaks:
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102 -algorithm:PrecursorSelection:exclude_overlapping_peaks
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103 #end if
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104 #if $param_algorithm_PrecursorSelection_Exclusion_use_dynamic_exclusion:
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105 -algorithm:PrecursorSelection:Exclusion:use_dynamic_exclusion
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106 #end if
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107 #if $param_algorithm_PrecursorSelection_Exclusion_exclusion_time:
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108 -algorithm:PrecursorSelection:Exclusion:exclusion_time $param_algorithm_PrecursorSelection_Exclusion_exclusion_time
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109 #end if
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110 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_max_list_size:
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111 -algorithm:PrecursorSelection:ProteinBasedInclusion:max_list_size $param_algorithm_PrecursorSelection_ProteinBasedInclusion_max_list_size
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112 #end if
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113 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_min_rt:
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114 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:min_rt $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_min_rt
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115 #end if
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116 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_max_rt:
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117 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:max_rt $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_max_rt
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118 #end if
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119 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_step_size:
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120 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_step_size $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_step_size
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121 #end if
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122 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_window_size:
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123 -algorithm:PrecursorSelection:ProteinBasedInclusion:rt:rt_window_size $param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_window_size
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124 #end if
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125 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_protein_id_probability:
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126 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_protein_id_probability $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_protein_id_probability
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127 #end if
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128 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_pt_weight:
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129 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_pt_weight $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_pt_weight
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130 #end if
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131 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_mz:
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132 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_mz $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_mz
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133 #end if
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134 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_max_mz:
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135 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:max_mz $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_max_mz
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136 #end if
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137 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_use_peptide_rule:
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138 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:use_peptide_rule
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139 #end if
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140 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_ids:
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141 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_ids $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_ids
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142 #end if
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143 #if $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_probability:
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144 -algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:min_peptide_probability $param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_probability
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145 #end if
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146 #if $param_algorithm_PrecursorSelection_feature_based_no_intensity_normalization:
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147 -algorithm:PrecursorSelection:feature_based:no_intensity_normalization
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148 #end if
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149 #if $param_algorithm_PrecursorSelection_feature_based_max_number_precursors_per_feature:
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150 -algorithm:PrecursorSelection:feature_based:max_number_precursors_per_feature $param_algorithm_PrecursorSelection_feature_based_max_number_precursors_per_feature
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151 #end if
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152 #if $adv_opts.adv_opts_selector=='advanced':
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153 #if $adv_opts.param_force:
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154 -force
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155 #end if
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156 #end if
0
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157 </command>
4
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158 <inputs>
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159 <param format="xml,fasta" help="(-include) " label="Inclusion list input file in FASTA or featureXML format" name="param_include" optional="True" type="data"/>
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160 <param format="xml,fasta" help="(-exclude) " label="Exclusion list input file in featureXML, idXML or FASTA format" name="param_exclude" optional="True" type="data"/>
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161 <param format="txt" help="(-rt_model) " label="RTModel file used for the rt prediction of peptides in FASTA files" name="param_rt_model" optional="True" type="data"/>
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162 <param format="txt" help="(-pt_model) " label="PTModel file used for the pt prediction of peptides in FASTA files (only needed for inclusion_strategy PreotinBased_LP)" name="param_pt_model" optional="True" type="data"/>
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163 <repeat min="0" name="rep_param_inclusion_charges" title="param_inclusion_charges">
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164 <param help="(-inclusion_charges) " label="List containing the charge states to be considered for the inclusion list compounds, space separated" min="1" name="param_inclusion_charges" optional="True" size="30" type="text" value="1">
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165 <sanitizer>
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166 <valid initial="string.printable">
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167 <remove value="'"/>
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168 <remove value="&quot;"/>
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169 </valid>
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170 </sanitizer>
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171 </param>
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172 </repeat>
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173 <param help="(-inclusion_strategy) " label="strategy to be used for selection" name="param_inclusion_strategy" optional="True" type="select" value="ALL">
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174 <option value="FeatureBased_LP">FeatureBased_LP</option>
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175 <option value="ProteinBased_LP">ProteinBased_LP</option>
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176 <option value="ALL">ALL</option>
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177 </param>
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178 <repeat min="0" name="rep_param_exclusion_charges" title="param_exclusion_charges">
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179 <param help="(-exclusion_charges) " label="List containing the charge states to be considered for the exclusion list compounds (for idXML and FASTA input), space separated" min="1" name="param_exclusion_charges" optional="True" size="30" type="text" value="1">
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180 <sanitizer>
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181 <valid initial="string.printable">
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182 <remove value="'"/>
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183 <remove value="&quot;"/>
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184 </valid>
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185 </sanitizer>
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186 </param>
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187 </repeat>
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188 <param format="mzml" help="(-raw_data) " label="File containing the raw data (only needed for FeatureBased_LP)" name="param_raw_data" optional="True" type="data"/>
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189 <param help="(-missed_cleavages) &lt;br&gt;" label="Number of missed cleavages used for protein digestion" name="param_algorithm_InclusionExclusionList_missed_cleavages" type="integer" value="0"/>
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190 <param help="(-unit) " label="Create lists with units as seconds instead of minutes" name="param_algorithm_InclusionExclusionList_RT_unit" optional="True" type="select" value="minutes">
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191 <option value="minutes">minutes</option>
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192 <option value="seconds">seconds</option>
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193 </param>
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194 <param checked="true" falsevalue="" help="(-use_relative) " label="Use relative RT window, which depends on RT of precurso" name="param_algorithm_InclusionExclusionList_RT_use_relative" optional="True" truevalue="-algorithm:InclusionExclusionList:RT:use_relative" type="boolean"/>
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195 <param help="(-window_relative) e.g. the window is calculated as [rt - rt*X, rt + rt*X]" label="[for RT:use_relative == true] The relative factor X for the RT exclusion window," max="10.0" min="0.0" name="param_algorithm_InclusionExclusionList_RT_window_relative" optional="True" type="float" value="0.05"/>
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196 <param help="(-window_absolute) e.g. the window is calculated as [rt - X, rt + X]" label="[for RT:use_relative == false] The absolute value X for the RT exclusion window in [sec]," min="0.0" name="param_algorithm_InclusionExclusionList_RT_window_absolute" optional="True" type="float" value="90.0"/>
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197 <param help="(-mz_tol) Unit of this is defined in 'mz_tol_unit'" 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" min="0.0" name="param_algorithm_InclusionExclusionList_merge_mz_tol" optional="True" type="float" value="10.0"/>
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198 <param help="(-mz_tol_unit) " label="Unit of 'mz_tol'" name="param_algorithm_InclusionExclusionList_merge_mz_tol_unit" optional="True" type="select" value="ppm">
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199 <option value="ppm">ppm</option>
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200 <option value="Da">Da</option>
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201 </param>
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202 <param 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]" label="Maximal RT delta (in seconds) which would allow two windows in RT to overlap (which causes merging the windows)" min="0.0" name="param_algorithm_InclusionExclusionList_merge_rt_tol" optional="True" type="float" value="1.1"/>
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203 <param help="(-ms2_spectra_per_rt_bin) " label="Number of allowed MS/MS spectra in a retention time bin" min="1" name="param_algorithm_PrecursorSelection_ms2_spectra_per_rt_bin" optional="True" type="integer" value="5"/>
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204 <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_PrecursorSelection_exclude_overlapping_peaks" optional="True" truevalue="-algorithm:PrecursorSelection:exclude_overlapping_peaks" type="boolean"/>
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205 <param checked="false" falsevalue="" help="(-use_dynamic_exclusion) " label="If true dynamic exclusion is applied" name="param_algorithm_PrecursorSelection_Exclusion_use_dynamic_exclusion" optional="True" truevalue="-algorithm:PrecursorSelection:Exclusion:use_dynamic_exclusion" type="boolean"/>
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206 <param help="(-exclusion_time) " label="The time (in seconds) a feature is excluded" min="0.0" name="param_algorithm_PrecursorSelection_Exclusion_exclusion_time" optional="True" type="float" value="100.0"/>
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207 <param help="(-max_list_size) " label="The maximal number of precursors in the inclusion list" min="1" name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_max_list_size" optional="True" type="integer" value="1000"/>
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208 <param help="(-min_rt) " label="Minimal rt in seconds" min="0.0" name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_min_rt" optional="True" type="float" value="960.0"/>
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209 <param help="(-max_rt) " label="Maximal rt in seconds" min="0.0" name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_max_rt" optional="True" type="float" value="3840.0"/>
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210 <param help="(-rt_step_size) " label="rt step size in seconds" min="1.0" name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_step_size" optional="True" type="float" value="30.0"/>
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211 <param help="(-rt_window_size) " label="rt window size in seconds" min="1" name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_rt_rt_window_size" optional="True" type="integer" value="100"/>
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212 <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_PrecursorSelection_ProteinBasedInclusion_thresholds_min_protein_id_probability" optional="True" type="float" value="0.95"/>
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213 <param help="(-min_pt_weight) " label="Minimal pt weight of a precurso" max="1.0" min="0.0" name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_pt_weight" optional="True" type="float" value="0.5"/>
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214 <param help="(-min_mz) " label="Minimal mz to be considered in protein based LP formulation" min="0.0" name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_min_mz" optional="True" type="float" value="500.0"/>
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215 <param help="(-max_mz) " label="Minimal mz to be considered in protein based LP formulation" min="0.0" name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_max_mz" optional="True" type="float" value="5000.0"/>
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216 <param checked="false" falsevalue="" help="(-use_peptide_rule) " label="Use peptide rule instead of minimal protein id probability" name="param_algorithm_PrecursorSelection_ProteinBasedInclusion_thresholds_use_peptide_rule" optional="True" truevalue="-algorithm:PrecursorSelection:ProteinBasedInclusion:thresholds:use_peptide_rule" type="boolean"/>
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217 <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_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_ids" optional="True" type="integer" value="2"/>
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218 <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_PrecursorSelection_ProteinBasedInclusion_thresholds_min_peptide_probability" optional="True" type="float" value="0.95"/>
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219 <param checked="false" falsevalue="" 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" label="Flag indicating if intensities shall be scaled to be in [0,1]" name="param_algorithm_PrecursorSelection_feature_based_no_intensity_normalization" optional="True" truevalue="-algorithm:PrecursorSelection:feature_based:no_intensity_normalization" type="boolean"/>
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220 <param help="(-max_number_precursors_per_feature) " label="The maximal number of precursors per feature" min="1" name="param_algorithm_PrecursorSelection_feature_based_max_number_precursors_per_feature" optional="True" type="integer" value="1"/>
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221 <expand macro="advanced_options">
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222 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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223 </expand>
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224 </inputs>
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225 <outputs>
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226 <data format="tabular" name="param_out"/>
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227 </outputs>
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228 <help>Creates inclusion and/or exclusion lists.
0
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229
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230
4
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231 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InclusionExclusionListCreator.html</help>
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232 </tool>