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annotate FileFilter.xml @ 0:c0bf230a772c draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 10:17:49 -0500
parents
children 2c3736b75339
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c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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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: [File Handling]-->
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4 <tool id="FileFilter" name="FileFilter" version="2.1.0">
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5 <description>Extracts or manipulates portions of data from peak, feature or consensus-feature files.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FileFilter</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>FileFilter
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14
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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15 #if $param_in:
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16 -in $param_in
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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 $param_out_type:
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22 -out_type
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23 #if " " in str($param_out_type):
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24 "$param_out_type"
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25 #else
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26 $param_out_type
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27 #end if
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28 #end if
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29 #if $param_rt:
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30 -rt "$param_rt"
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31 #end if
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32 #if $param_mz:
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33 -mz "$param_mz"
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34 #end if
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35 #if $param_int:
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36 -int "$param_int"
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37 #end if
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38 #if $param_sort:
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39 -sort
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40 #end if
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41 #if $param_peak_options_sn:
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42 -peak_options:sn $param_peak_options_sn
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43 #end if
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44
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45 #if $rep_param_peak_options_rm_pc_charge:
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46 -peak_options:rm_pc_charge
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47 #for token in $rep_param_peak_options_rm_pc_charge:
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48 #if " " in str(token):
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49 "$token.param_peak_options_rm_pc_charge"
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50 #else
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51 $token.param_peak_options_rm_pc_charge
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52 #end if
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53 #end for
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54 #end if
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55 #if $param_peak_options_pc_mz_range:
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56 -peak_options:pc_mz_range "$param_peak_options_pc_mz_range"
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57 #end if
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58
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59 #if $rep_param_peak_options_pc_mz_list:
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60 -peak_options:pc_mz_list
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61 #for token in $rep_param_peak_options_pc_mz_list:
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62 #if " " in str(token):
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63 "$token.param_peak_options_pc_mz_list"
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64 #else
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65 $token.param_peak_options_pc_mz_list
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66 #end if
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67 #end for
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68 #end if
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69
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70 #if $rep_param_peak_options_level:
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71 -peak_options:level
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72 #for token in $rep_param_peak_options_level:
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73 #if " " in str(token):
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74 "$token.param_peak_options_level"
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75 #else
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76 $token.param_peak_options_level
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77 #end if
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78 #end for
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79 #end if
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80 #if $param_peak_options_sort_peaks:
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81 -peak_options:sort_peaks
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82 #end if
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83 #if $param_peak_options_no_chromatograms:
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84 -peak_options:no_chromatograms
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85 #end if
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86 #if $param_peak_options_remove_chromatograms:
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87 -peak_options:remove_chromatograms
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88 #end if
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89 #if $param_peak_options_mz_precision:
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90 -peak_options:mz_precision $param_peak_options_mz_precision
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91 #end if
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92 #if $param_peak_options_int_precision:
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93 -peak_options:int_precision $param_peak_options_int_precision
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94 #end if
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95 #if $param_peak_options_indexed_file:
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96 -peak_options:indexed_file
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97 #end if
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98 #if $param_peak_options_numpress_masstime:
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99 -peak_options:numpress:masstime $param_peak_options_numpress_masstime
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100 #end if
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101 #if $param_peak_options_numpress_masstime_error:
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102 -peak_options:numpress:masstime_error $param_peak_options_numpress_masstime_error
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103 #end if
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104 #if $param_peak_options_numpress_intensity:
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105 -peak_options:numpress:intensity $param_peak_options_numpress_intensity
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106 #end if
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107 #if $param_peak_options_numpress_intensity_error:
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108 -peak_options:numpress:intensity_error $param_peak_options_numpress_intensity_error
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109 #end if
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110 #if $param_spectra_remove_zoom:
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111 -spectra:remove_zoom
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112 #end if
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113 #if $param_spectra_remove_mode:
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114 -spectra:remove_mode
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115 #if " " in str($param_spectra_remove_mode):
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116 "$param_spectra_remove_mode"
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117 #else
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118 $param_spectra_remove_mode
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119 #end if
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120 #end if
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121 #if $param_spectra_remove_activation:
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122 -spectra:remove_activation
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123 #if " " in str($param_spectra_remove_activation):
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124 "$param_spectra_remove_activation"
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125 #else
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126 $param_spectra_remove_activation
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127 #end if
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128 #end if
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129 #if $param_spectra_remove_collision_energy:
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130 -spectra:remove_collision_energy "$param_spectra_remove_collision_energy"
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131 #end if
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132 #if $param_spectra_remove_isolation_window_width:
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133 -spectra:remove_isolation_window_width "$param_spectra_remove_isolation_window_width"
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134 #end if
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135 #if $param_spectra_select_zoom:
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136 -spectra:select_zoom
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137 #end if
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138 #if $param_spectra_select_mode:
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139 -spectra:select_mode
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140 #if " " in str($param_spectra_select_mode):
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141 "$param_spectra_select_mode"
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142 #else
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143 $param_spectra_select_mode
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144 #end if
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145 #end if
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146 #if $param_spectra_select_activation:
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147 -spectra:select_activation
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148 #if " " in str($param_spectra_select_activation):
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149 "$param_spectra_select_activation"
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150 #else
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151 $param_spectra_select_activation
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152 #end if
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153 #end if
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154 #if $param_spectra_select_collision_energy:
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155 -spectra:select_collision_energy "$param_spectra_select_collision_energy"
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156 #end if
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157 #if $param_spectra_select_isolation_window_width:
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158 -spectra:select_isolation_window_width "$param_spectra_select_isolation_window_width"
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159 #end if
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160 #if $param_spectra_select_polarity:
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161 -spectra:select_polarity
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162 #if " " in str($param_spectra_select_polarity):
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163 "$param_spectra_select_polarity"
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164 #else
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165 $param_spectra_select_polarity
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166 #end if
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167 #end if
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168 #if $param_feature_q:
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169 -feature:q "$param_feature_q"
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170 #end if
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171
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172 #if $rep_param_consensus_map:
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173 -consensus:map
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174 #for token in $rep_param_consensus_map:
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175 #if " " in str(token):
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176 "$token.param_consensus_map"
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177 #else
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178 $token.param_consensus_map
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galaxyp
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diff changeset
179 #end if
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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180 #end for
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diff changeset
181 #end if
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
182 #if $param_consensus_map_and:
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galaxyp
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diff changeset
183 -consensus:map_and
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diff changeset
184 #end if
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galaxyp
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diff changeset
185 #if $param_consensus_blackorwhitelist_blacklist:
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galaxyp
parents:
diff changeset
186 -consensus:blackorwhitelist:blacklist $param_consensus_blackorwhitelist_blacklist
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
187 #end if
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galaxyp
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diff changeset
188 #if $param_consensus_blackorwhitelist_file:
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galaxyp
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diff changeset
189 -consensus:blackorwhitelist:file $param_consensus_blackorwhitelist_file
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
190 #end if
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
191
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
192 #if $rep_param_consensus_blackorwhitelist_maps:
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galaxyp
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diff changeset
193 -consensus:blackorwhitelist:maps
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galaxyp
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diff changeset
194 #for token in $rep_param_consensus_blackorwhitelist_maps:
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galaxyp
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diff changeset
195 #if " " in str(token):
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galaxyp
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diff changeset
196 "$token.param_consensus_blackorwhitelist_maps"
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197 #else
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galaxyp
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diff changeset
198 $token.param_consensus_blackorwhitelist_maps
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199 #end if
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galaxyp
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diff changeset
200 #end for
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galaxyp
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diff changeset
201 #end if
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
202 #if $param_consensus_blackorwhitelist_rt:
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galaxyp
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diff changeset
203 -consensus:blackorwhitelist:rt $param_consensus_blackorwhitelist_rt
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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204 #end if
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galaxyp
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diff changeset
205 #if $param_consensus_blackorwhitelist_mz:
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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206 -consensus:blackorwhitelist:mz $param_consensus_blackorwhitelist_mz
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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207 #end if
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
208 #if $param_consensus_blackorwhitelist_use_ppm_tolerance:
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galaxyp
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diff changeset
209 -consensus:blackorwhitelist:use_ppm_tolerance
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
210 #end if
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galaxyp
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211 #if $param_f_and_c_charge:
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galaxyp
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212 -f_and_c:charge "$param_f_and_c_charge"
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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213 #end if
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galaxyp
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214 #if $param_f_and_c_size:
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galaxyp
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215 -f_and_c:size "$param_f_and_c_size"
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216 #end if
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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217
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galaxyp
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218 #if $rep_param_f_and_c_remove_meta:
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galaxyp
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219 -f_and_c:remove_meta
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galaxyp
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220 #for token in $rep_param_f_and_c_remove_meta:
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galaxyp
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diff changeset
221 #if " " in str(token):
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galaxyp
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222 "$token.param_f_and_c_remove_meta"
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diff changeset
223 #else
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galaxyp
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diff changeset
224 $token.param_f_and_c_remove_meta
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galaxyp
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diff changeset
225 #end if
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galaxyp
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diff changeset
226 #end for
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galaxyp
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227 #end if
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galaxyp
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228 #if $param_id_keep_best_score_id:
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galaxyp
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229 -id:keep_best_score_id
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galaxyp
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diff changeset
230 #end if
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galaxyp
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231
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galaxyp
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232 #if $rep_param_id_sequences_whitelist:
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galaxyp
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diff changeset
233 -id:sequences_whitelist
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galaxyp
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diff changeset
234 #for token in $rep_param_id_sequences_whitelist:
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
235 #if " " in str(token):
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
236 "$token.param_id_sequences_whitelist"
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
237 #else
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galaxyp
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diff changeset
238 $token.param_id_sequences_whitelist
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
239 #end if
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
240 #end for
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
241 #end if
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
242
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
243 #if $rep_param_id_accessions_whitelist:
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
244 -id:accessions_whitelist
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
245 #for token in $rep_param_id_accessions_whitelist:
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
246 #if " " in str(token):
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
247 "$token.param_id_accessions_whitelist"
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
248 #else
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
249 $token.param_id_accessions_whitelist
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
250 #end if
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
251 #end for
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
252 #end if
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
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253 #if $param_id_remove_annotated_features:
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
254 -id:remove_annotated_features
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
255 #end if
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
256 #if $param_id_remove_unannotated_features:
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
257 -id:remove_unannotated_features
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
258 #end if
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
259 #if $param_id_remove_unassigned_ids:
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
260 -id:remove_unassigned_ids
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
261 #end if
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
262 #if $param_id_blacklist:
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
263 -id:blacklist $param_id_blacklist
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
264 #end if
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
265 #if $param_id_rt:
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
266 -id:rt $param_id_rt
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
267 #end if
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
268 #if $param_id_mz:
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
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269 -id:mz $param_id_mz
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270 #end if
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271 #if $param_id_blacklist_imperfect:
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272 -id:blacklist_imperfect
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273 #end if
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274 #if $param_algorithm_SignalToNoise_win_len:
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275 -algorithm:SignalToNoise:win_len $param_algorithm_SignalToNoise_win_len
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276 #end if
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277 #if $param_algorithm_SignalToNoise_bin_count:
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278 -algorithm:SignalToNoise:bin_count $param_algorithm_SignalToNoise_bin_count
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279 #end if
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280 #if $param_algorithm_SignalToNoise_min_required_elements:
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281 -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements
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282 #end if
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283 #if $param_algorithm_SignalToNoise_write_log_messages:
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284 -algorithm:SignalToNoise:write_log_messages $param_algorithm_SignalToNoise_write_log_messages
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285 #end if
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286 #if $adv_opts.adv_opts_selector=='advanced':
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287 #if $adv_opts.param_force:
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288 -force
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289 #end if
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290 #if $adv_opts.param_id_remove_clashes:
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291 -id:remove_clashes
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292 #end if
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293 #if $adv_opts.param_algorithm_SignalToNoise_max_intensity:
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294 -algorithm:SignalToNoise:max_intensity $adv_opts.param_algorithm_SignalToNoise_max_intensity
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295 #end if
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296 #if $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor:
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297 -algorithm:SignalToNoise:auto_max_stdev_factor $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor
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298 #end if
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299 #if $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile:
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300 -algorithm:SignalToNoise:auto_max_percentile $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile
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301 #end if
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302 #if $adv_opts.param_algorithm_SignalToNoise_auto_mode:
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303 -algorithm:SignalToNoise:auto_mode $adv_opts.param_algorithm_SignalToNoise_auto_mode
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304 #end if
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305 #if $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window:
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306 -algorithm:SignalToNoise:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window
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307 #end if
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308 #end if
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309 </command>
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310 <inputs>
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311 <param name="param_in" type="data" format="featurexml,consensusxml,mzml" optional="False" label="Input file" help="(-in) "/>
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312 <param name="param_out_type" display="radio" type="select" optional="True" label="Output file type -- default: determined from file extension or content" help="(-out_type) ">
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313 <option value="mzML">mzML</option>
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314 <option value="featureXML">featureXML</option>
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315 <option value="consensusXML">consensusXML</option>
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316 </param>
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317 <param name="param_rt" type="text" size="30" value=":" label="Retention time range to extract" help="(-rt) ">
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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="&quot;"/>
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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_mz" type="text" size="30" value=":" label="m/z range to extract (applies to ALL ms levels!)" help="(-mz) ">
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326 <sanitizer>
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327 <valid initial="string.printable">
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328 <remove value="'"/>
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329 <remove value="&quot;"/>
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330 </valid>
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331 </sanitizer>
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332 </param>
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333 <param name="param_int" type="text" size="30" value=":" label="Intensity range to extract" help="(-int) ">
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334 <sanitizer>
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335 <valid initial="string.printable">
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336 <remove value="'"/>
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337 <remove value="&quot;"/>
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338 </valid>
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339 </sanitizer>
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340 </param>
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341 <param name="param_sort" display="radio" type="boolean" truevalue="-sort" falsevalue="" checked="false" optional="True" label="Sorts the output according to RT and m/z" help="(-sort) "/>
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342 <param name="param_peak_options_sn" type="float" value="0.0" label="Write peaks with S/N &gt; 'sn' values only" help="(-sn) "/>
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343 <repeat name="rep_param_peak_options_rm_pc_charge" min="0" max="1" title="param_peak_options_rm_pc_charge">
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344 <param name="param_peak_options_rm_pc_charge" type="text" size="30" value="0" label="Remove MS(2) spectra with these precursor charges" help="(-rm_pc_charge) All spectra without precursor are kept!">
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345 <sanitizer>
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346 <valid initial="string.printable">
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347 <remove value="'"/>
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348 <remove value="&quot;"/>
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349 </valid>
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350 </sanitizer>
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351 </param>
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352 </repeat>
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353 <param name="param_peak_options_pc_mz_range" type="text" size="30" value=":" label="MSn (n&gt;=2) precursor filtering according to their m/z value" help="(-pc_mz_range) Do not use this flag in conjunction with 'mz', unless you want to actually remove peaks in spectra (see 'mz'). RT filtering is covered by 'rt' and compatible with this flag">
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354 <sanitizer>
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galaxyp
parents:
diff changeset
355 <valid initial="string.printable">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
356 <remove value="'"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
357 <remove value="&quot;"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff changeset
358 </valid>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff changeset
359 </sanitizer>
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parents:
diff changeset
360 </param>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff changeset
361 <repeat name="rep_param_peak_options_pc_mz_list" min="0" max="1" title="param_peak_options_pc_mz_list">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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362 <param name="param_peak_options_pc_mz_list" type="text" size="30" value="0" label="List of m/z values" help="(-pc_mz_list) If a precursor window covers ANY of these values, the corresponding MS/MS spectrum will be kept">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
363 <sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
364 <valid initial="string.printable">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
365 <remove value="'"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
366 <remove value="&quot;"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff changeset
367 </valid>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff changeset
368 </sanitizer>
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diff changeset
369 </param>
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diff changeset
370 </repeat>
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371 <repeat name="rep_param_peak_options_level" min="0" max="1" title="param_peak_options_level">
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372 <param name="param_peak_options_level" type="text" size="30" value="1 2 3" label="MS levels to extract" help="(-level) ">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
373 <sanitizer>
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parents:
diff changeset
374 <valid initial="string.printable">
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parents:
diff changeset
375 <remove value="'"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
376 <remove value="&quot;"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
377 </valid>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff changeset
378 </sanitizer>
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diff changeset
379 </param>
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diff changeset
380 </repeat>
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381 <param name="param_peak_options_sort_peaks" display="radio" type="boolean" truevalue="-peak_options:sort_peaks" falsevalue="" checked="false" optional="True" label="Sorts the peaks according to m/z" help="(-sort_peaks) "/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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382 <param name="param_peak_options_no_chromatograms" display="radio" type="boolean" truevalue="-peak_options:no_chromatograms" falsevalue="" checked="false" optional="True" label="No conversion to space-saving real chromatograms," help="(-no_chromatograms) e.g. from SRM scans"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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383 <param name="param_peak_options_remove_chromatograms" display="radio" type="boolean" truevalue="-peak_options:remove_chromatograms" falsevalue="" checked="false" optional="True" label="Removes chromatograms stored in a file" help="(-remove_chromatograms) "/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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384 <param name="param_peak_options_mz_precision" display="radio" type="select" optional="False" value="64" label="Store base64 encoded m/z data using 32 or 64 bit precision" help="(-mz_precision) ">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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385 <option value="32">32</option>
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386 <option value="64" selected="true">64</option>
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diff changeset
387 </param>
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388 <param name="param_peak_options_int_precision" display="radio" type="select" optional="False" value="32" label="Store base64 encoded intensity data using 32 or 64 bit precision" help="(-int_precision) ">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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389 <option value="32" selected="true">32</option>
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390 <option value="64">64</option>
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diff changeset
391 </param>
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392 <param name="param_peak_options_indexed_file" display="radio" type="boolean" truevalue="-peak_options:indexed_file" falsevalue="" checked="false" optional="True" label="Whether to add an index to the file when writing" help="(-indexed_file) "/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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393 <param name="param_peak_options_numpress_masstime" display="radio" type="select" optional="False" value="none" label="Apply MS Numpress compression algorithms in m/z or rt dimension (recommended: linear)" help="(-masstime) ">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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394 <option value="none" selected="true">none</option>
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395 <option value="linear">linear</option>
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396 <option value="pic">pic</option>
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397 <option value="slof">slof</option>
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diff changeset
398 </param>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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399 <param name="param_peak_options_numpress_masstime_error" type="float" value="0.0001" label="Maximal allowable error in m/z or rt dimension (set to 0.5 for pic)" help="(-masstime_error) "/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
400 <param name="param_peak_options_numpress_intensity" display="radio" type="select" optional="False" value="none" label="Apply MS Numpress compression algorithms in intensity dimension (recommended: slof or pic)" help="(-intensity) ">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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parents:
diff changeset
401 <option value="none" selected="true">none</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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diff changeset
402 <option value="linear">linear</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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403 <option value="pic">pic</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
404 <option value="slof">slof</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
405 </param>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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406 <param name="param_peak_options_numpress_intensity_error" type="float" value="0.0001" label="Maximal allowable error in intensity dimension (set to 0.5 for pic)" help="(-intensity_error) "/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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407 <param name="param_spectra_remove_zoom" display="radio" type="boolean" truevalue="-spectra:remove_zoom" falsevalue="" checked="false" optional="True" label="Remove zoom (enhanced resolution) scans" help="(-remove_zoom) "/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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408 <param name="param_spectra_remove_mode" type="select" optional="True" label="Remove scans by scan mode" help="(-remove_mode) ">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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409 <option value="Unknown">Unknown</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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410 <option value="MassSpectrum">MassSpectrum</option>
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411 <option value="MS1Spectrum">MS1Spectrum</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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412 <option value="MSnSpectrum">MSnSpectrum</option>
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413 <option value="SelectedIonMonitoring">SelectedIonMonitoring</option>
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414 <option value="SelectedReactionMonitoring">SelectedReactionMonitoring</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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415 <option value="ConsecutiveReactionMonitoring">ConsecutiveReactionMonitoring</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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416 <option value="ConstantNeutralGain">ConstantNeutralGain</option>
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417 <option value="ConstantNeutralLoss">ConstantNeutralLoss</option>
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418 <option value="Precursor">Precursor</option>
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419 <option value="EnhancedMultiplyCharged">EnhancedMultiplyCharged</option>
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420 <option value="TimeDelayedFragmentation">TimeDelayedFragmentation</option>
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421 <option value="ElectromagneticRadiation">ElectromagneticRadiation</option>
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422 <option value="Emission">Emission</option>
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423 <option value="Absorbtion">Absorbtion</option>
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424 </param>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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425 <param name="param_spectra_remove_activation" type="select" optional="True" label="Remove MSn scans where any of its precursors features a certain activation method" help="(-remove_activation) ">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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426 <option value="Collision-induced dissociation">Collision-induced dissociation</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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427 <option value="Post-source decay">Post-source decay</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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428 <option value="Plasma desorption">Plasma desorption</option>
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429 <option value="Surface-induced dissociation">Surface-induced dissociation</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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430 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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431 <option value="Electron capture dissociation">Electron capture dissociation</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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432 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option>
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433 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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diff changeset
434 <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
435 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
436 <option value="Photodissociation">Photodissociation</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
437 <option value="Electron transfer dissociation">Electron transfer dissociation</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
438 <option value="Pulsed q dissociation">Pulsed q dissociation</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
439 </param>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
440 <param name="param_spectra_remove_collision_energy" type="text" size="30" value=":" label="Remove MSn scans with a collision energy in the given interval" help="(-remove_collision_energy) ">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
441 <sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
442 <valid initial="string.printable">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
443 <remove value="'"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
444 <remove value="&quot;"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
445 </valid>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
446 </sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
447 </param>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
448 <param name="param_spectra_remove_isolation_window_width" type="text" size="30" value=":" label="Remove MSn scans whose isolation window width is in the given interval" help="(-remove_isolation_window_width) ">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
449 <sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
450 <valid initial="string.printable">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
451 <remove value="'"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
452 <remove value="&quot;"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
453 </valid>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
454 </sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
455 </param>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
456 <param name="param_spectra_select_zoom" display="radio" type="boolean" truevalue="-spectra:select_zoom" falsevalue="" checked="false" optional="True" label="Select zoom (enhanced resolution) scans" help="(-select_zoom) "/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
457 <param name="param_spectra_select_mode" type="select" optional="True" label="Selects scans by scan mode" help="(-select_mode) ">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
458 <option value="Unknown">Unknown</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
459 <option value="MassSpectrum">MassSpectrum</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
460 <option value="MS1Spectrum">MS1Spectrum</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
461 <option value="MSnSpectrum">MSnSpectrum</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
462 <option value="SelectedIonMonitoring">SelectedIonMonitoring</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
463 <option value="SelectedReactionMonitoring">SelectedReactionMonitoring</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
464 <option value="ConsecutiveReactionMonitoring">ConsecutiveReactionMonitoring</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
465 <option value="ConstantNeutralGain">ConstantNeutralGain</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
466 <option value="ConstantNeutralLoss">ConstantNeutralLoss</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
467 <option value="Precursor">Precursor</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
468 <option value="EnhancedMultiplyCharged">EnhancedMultiplyCharged</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
469 <option value="TimeDelayedFragmentation">TimeDelayedFragmentation</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
470 <option value="ElectromagneticRadiation">ElectromagneticRadiation</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
471 <option value="Emission">Emission</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
472 <option value="Absorbtion">Absorbtion</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
473 </param>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
474 <param name="param_spectra_select_activation" type="select" optional="True" label="Retain MSn scans where any of its precursors features a certain activation method" help="(-select_activation) ">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
475 <option value="Collision-induced dissociation">Collision-induced dissociation</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
476 <option value="Post-source decay">Post-source decay</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
477 <option value="Plasma desorption">Plasma desorption</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
478 <option value="Surface-induced dissociation">Surface-induced dissociation</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
479 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
480 <option value="Electron capture dissociation">Electron capture dissociation</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
481 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
482 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
483 <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
484 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
485 <option value="Photodissociation">Photodissociation</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
486 <option value="Electron transfer dissociation">Electron transfer dissociation</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
487 <option value="Pulsed q dissociation">Pulsed q dissociation</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
488 </param>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
489 <param name="param_spectra_select_collision_energy" type="text" size="30" value=":" label="Select MSn scans with a collision energy in the given interval" help="(-select_collision_energy) ">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
490 <sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
491 <valid initial="string.printable">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
492 <remove value="'"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
493 <remove value="&quot;"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
494 </valid>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
495 </sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
496 </param>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
497 <param name="param_spectra_select_isolation_window_width" type="text" size="30" value=":" label="Select MSn scans whose isolation window width is in the given interval" help="(-select_isolation_window_width) ">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
498 <sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
499 <valid initial="string.printable">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
500 <remove value="'"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
501 <remove value="&quot;"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
502 </valid>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
503 </sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
504 </param>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
505 <param name="param_spectra_select_polarity" display="radio" type="select" optional="True" label="Retain MSn scans with a certain scan polarity" help="(-select_polarity) ">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
506 <option value="unknown">unknown</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
507 <option value="positive">positive</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
508 <option value="negative">negative</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
509 </param>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
510 <param name="param_feature_q" type="text" size="30" value=":" label="Overall quality range to extract [0:1]" help="(-q) ">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
511 <sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
512 <valid initial="string.printable">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
513 <remove value="'"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
514 <remove value="&quot;"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
515 </valid>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
516 </sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
517 </param>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
518 <repeat name="rep_param_consensus_map" min="0" max="1" title="param_consensus_map">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
519 <param name="param_consensus_map" type="text" size="30" value="0" label="Maps to be extracted from a consensus" help="(-map) ">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
520 <sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
521 <valid initial="string.printable">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
522 <remove value="'"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
523 <remove value="&quot;"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
524 </valid>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
525 </sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
526 </param>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
527 </repeat>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
528 <param name="param_consensus_map_and" display="radio" type="boolean" truevalue="-consensus:map_and" falsevalue="" checked="false" optional="True" label="Consensus features are kept only if they contain exactly one feature from each map (as given above in 'map')" help="(-map_and) "/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
529 <param name="param_consensus_blackorwhitelist_blacklist" display="radio" type="select" optional="False" value="true" label="True: remove matched MS2" help="(-blacklist) False: retain matched MS2 spectra. Other levels are kept">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
530 <option value="false">false</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
531 <option value="true" selected="true">true</option>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
532 </param>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
533 <param name="param_consensus_blackorwhitelist_file" type="data" format="consensusxml" optional="True" label="Input file containing consensus features whose corresponding MS2 spectra should be removed from the mzML file! &lt;br&gt;Matching tolerances are taken from 'consensus:blackorwhitelist:rt' and 'consensus:blackorwhitelist:mz' options" help="(-file) &lt;br&gt;If consensus:blackorwhitelist:maps is specified, only these will be used. &lt;br&gt;"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
534 <repeat name="rep_param_consensus_blackorwhitelist_maps" min="0" max="1" title="param_consensus_blackorwhitelist_maps">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
535 <param name="param_consensus_blackorwhitelist_maps" type="text" size="30" value="0" label="Maps used for black/white list filtering" help="(-maps) ">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
536 <sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
537 <valid initial="string.printable">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
538 <remove value="'"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
539 <remove value="&quot;"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
540 </valid>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
541 </sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
542 </param>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
543 </repeat>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
544 <param name="param_consensus_blackorwhitelist_rt" type="float" min="0.0" optional="True" value="60.0" label="Retention tolerance [s] for precursor to consensus feature position" help="(-rt) "/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
545 <param name="param_consensus_blackorwhitelist_mz" type="float" min="0.0" optional="True" value="0.01" label="m/z tolerance [Th] for precursor to consensus feature position" help="(-mz) "/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
546 <param name="param_consensus_blackorwhitelist_use_ppm_tolerance" display="radio" type="boolean" truevalue="-consensus:blackorwhitelist:use_ppm_tolerance" falsevalue="" checked="false" optional="True" label="If ppm tolerance should be used" help="(-use_ppm_tolerance) Otherwise Da are used"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
547 <param name="param_f_and_c_charge" type="text" size="30" value=":" label="Charge range to extract" help="(-charge) ">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
548 <sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
549 <valid initial="string.printable">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
550 <remove value="'"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
551 <remove value="&quot;"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
552 </valid>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
553 </sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
554 </param>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
555 <param name="param_f_and_c_size" type="text" size="30" value=":" label="Size range to extract" help="(-size) ">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
556 <sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
557 <valid initial="string.printable">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
558 <remove value="'"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
559 <remove value="&quot;"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
560 </valid>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
561 </sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
562 </param>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
563 <repeat name="rep_param_f_and_c_remove_meta" min="0" max="1" title="param_f_and_c_remove_meta">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
564 <param name="param_f_and_c_remove_meta" type="text" size="30" label="Expects a 3-tuple (=3 entries in the list), i.e" help="(-remove_meta) &lt;name&gt; 'lt|eq|gt' &lt;value&gt;; the first is the name of meta value, followed by the comparison operator (equal, less or greater) and the value to compare to. All comparisons are done after converting the given value to the corresponding data value type of the meta value (for lists, this simply compares length, not content!)!">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
565 <sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
566 <valid initial="string.printable">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
567 <remove value="'"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
568 <remove value="&quot;"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
569 </valid>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
570 </sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
571 </param>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
572 </repeat>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
573 <param name="param_id_keep_best_score_id" display="radio" type="boolean" truevalue="-id:keep_best_score_id" falsevalue="" checked="false" optional="True" label="in case of multiple peptide identifications, keep only the id with best score" help="(-keep_best_score_id) "/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
574 <repeat name="rep_param_id_sequences_whitelist" min="0" max="1" title="param_id_sequences_whitelist">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
575 <param name="param_id_sequences_whitelist" type="text" size="30" label="keep only features with white listed sequences," help="(-sequences_whitelist) e.g. LYSNLVER or the modification (Oxidation)">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
576 <sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
577 <valid initial="string.printable">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
578 <remove value="'"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
579 <remove value="&quot;"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
580 </valid>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
581 </sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
582 </param>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
583 </repeat>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
584 <repeat name="rep_param_id_accessions_whitelist" min="0" max="1" title="param_id_accessions_whitelist">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
585 <param name="param_id_accessions_whitelist" type="text" size="30" label="keep only features with white listed accessions," help="(-accessions_whitelist) e.g. sp|P02662|CASA1_BOVIN">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
586 <sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
587 <valid initial="string.printable">
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
588 <remove value="'"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
589 <remove value="&quot;"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
590 </valid>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
591 </sanitizer>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
592 </param>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
593 </repeat>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
594 <param name="param_id_remove_annotated_features" display="radio" type="boolean" truevalue="-id:remove_annotated_features" falsevalue="" checked="false" optional="True" label="Remove features with annotations" help="(-remove_annotated_features) "/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
595 <param name="param_id_remove_unannotated_features" display="radio" type="boolean" truevalue="-id:remove_unannotated_features" falsevalue="" checked="false" optional="True" label="Remove features without annotations" help="(-remove_unannotated_features) "/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
596 <param name="param_id_remove_unassigned_ids" display="radio" type="boolean" truevalue="-id:remove_unassigned_ids" falsevalue="" checked="false" optional="True" label="Remove unassigned peptide identifications" help="(-remove_unassigned_ids) "/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
parents:
diff changeset
597 <param name="param_id_blacklist" type="data" format="idxml" optional="True" label="Input file containing MS2 identifications whose corresponding MS2 spectra should be removed from the mzML file! &lt;br&gt;Matching tolerances are taken from 'id:rt' and 'id:mz' options" help="(-blacklist) &lt;br&gt;This tool will require all IDs to be matched to an MS2 spectrum, and quit with error otherwise. Use 'id:blacklist_imperfect' to allow for mismatches"/>
c0bf230a772c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
galaxyp
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598 <param name="param_id_rt" type="float" min="0.0" optional="True" value="0.1" label="Retention tolerance [s] for precursor to id position" help="(-rt) "/>
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599 <param name="param_id_mz" type="float" min="0.0" optional="True" value="0.001" label="m/z tolerance [Th] for precursor to id position" help="(-mz) "/>
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600 <param name="param_id_blacklist_imperfect" display="radio" type="boolean" truevalue="-id:blacklist_imperfect" falsevalue="" checked="false" optional="True" label="Allow for mismatching precursor positions (see 'id:blacklist')" help="(-blacklist_imperfect) "/>
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601 <param name="param_algorithm_SignalToNoise_win_len" type="float" min="1.0" optional="True" value="200.0" label="window length in Thomson" help="(-win_len) "/>
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602 <param name="param_algorithm_SignalToNoise_bin_count" type="integer" min="3" optional="True" value="30" label="number of bins for intensity values" help="(-bin_count) "/>
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603 <param name="param_algorithm_SignalToNoise_min_required_elements" type="integer" min="1" optional="True" value="10" label="minimum number of elements required in a window (otherwise it is considered sparse)" help="(-min_required_elements) "/>
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604 <param name="param_algorithm_SignalToNoise_write_log_messages" display="radio" type="select" optional="False" value="true" label="Write out log messages in case of sparse windows or median in rightmost histogram bin" help="(-write_log_messages) ">
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605 <option value="true" selected="true">true</option>
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606 <option value="false">false</option>
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607 </param>
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608 <expand macro="advanced_options">
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609 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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610 <param name="param_id_remove_clashes" display="radio" type="boolean" truevalue="-id:remove_clashes" falsevalue="" checked="false" optional="True" label="Remove features with id clashes (different sequences mapped to one feature)" help="(-remove_clashes) "/>
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611 <param name="param_algorithm_SignalToNoise_max_intensity" type="integer" min="-1" optional="True" value="-1" label="maximal intensity considered for histogram construction" help="(-max_intensity) By default, it will be calculated automatically (see auto_mode). Only provide this parameter if you know what you are doing (and change 'auto_mode' to '-1')! All intensities EQUAL/ABOVE 'max_intensity' will be added to the LAST histogram bin. If you choose 'max_intensity' too small, the noise estimate might be too small as well. If chosen too big, the bins become quite large (which you could counter by increasing 'bin_count', which increases runtime). In general, the Median-S/N estimator is more robust to a manual max_intensity than the MeanIterative-S/N"/>
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612 <param name="param_algorithm_SignalToNoise_auto_max_stdev_factor" type="float" min="0.0" max="999.0" optional="True" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help="(-auto_max_stdev_factor) "/>
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613 <param name="param_algorithm_SignalToNoise_auto_max_percentile" type="integer" min="0" max="100" optional="True" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help="(-auto_max_percentile) "/>
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614 <param name="param_algorithm_SignalToNoise_auto_mode" type="integer" min="-1" max="1" optional="True" value="0" label="method to use to determine maximal intensity: -1 --&gt; use 'max_intensity'; 0 --&gt; 'auto_max_stdev_factor' method (default); 1 --&gt; 'auto_max_percentile' method" help="(-auto_mode) "/>
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615 <param name="param_algorithm_SignalToNoise_noise_for_empty_window" type="float" value="1e+20" label="noise value used for sparse windows" help="(-noise_for_empty_window) "/>
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616 </expand>
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617 </inputs>
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618 <outputs>
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619 <data name="param_out" metadata_source="param_in" format="input"/>
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620 </outputs>
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621 <help>Extracts or manipulates portions of data from peak, feature or consensus-feature files.
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622
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623
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624 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileFilter.html</help>
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625 </tool>