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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="2.0.0">
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3 <description>Calculates isobaric quantitative values for peptides</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">IsobaricAnalyzer</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>IsobaricAnalyzer
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11
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12 #if $param_type:
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13 -type
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14 #if " " in str($param_type):
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15 "$param_type"
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16 #else
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17 $param_type
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18 #end if
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19 #end if
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20 #if $param_in:
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21 -in $param_in
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22 #end if
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23 #if $param_out:
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24 -out $param_out
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25 #end if
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26 -threads \${GALAXY_SLOTS:-24}
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27 #if $param_id_pool:
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28 -id_pool "$param_id_pool"
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29 #end if
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30 #if $param_extraction_select_activation:
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31 -extraction:select_activation
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32 #if " " in str($param_extraction_select_activation):
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33 "$param_extraction_select_activation"
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34 #else
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35 $param_extraction_select_activation
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36 #end if
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37 #end if
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38 #if $param_extraction_reporter_mass_shift:
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39 -extraction:reporter_mass_shift $param_extraction_reporter_mass_shift
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40 #end if
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41 #if $param_extraction_min_precursor_intensity:
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42 -extraction:min_precursor_intensity $param_extraction_min_precursor_intensity
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43 #end if
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44 #if $param_extraction_keep_unannotated_precursor:
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45 -extraction:keep_unannotated_precursor
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46 #end if
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47 #if $param_extraction_min_reporter_intensity:
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48 -extraction:min_reporter_intensity $param_extraction_min_reporter_intensity
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49 #end if
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50 #if $param_extraction_discard_low_intensity_quantifications:
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51 -extraction:discard_low_intensity_quantifications
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52 #end if
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53 #if $param_extraction_min_precursor_purity:
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54 -extraction:min_precursor_purity $param_extraction_min_precursor_purity
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55 #end if
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56 #if $param_itraq4plex_channel_114_description:
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57 -itraq4plex:channel_114_description "$param_itraq4plex_channel_114_description"
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58 #end if
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59 #if $param_itraq4plex_channel_115_description:
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60 -itraq4plex:channel_115_description "$param_itraq4plex_channel_115_description"
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61 #end if
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62 #if $param_itraq4plex_channel_116_description:
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63 -itraq4plex:channel_116_description "$param_itraq4plex_channel_116_description"
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64 #end if
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65 #if $param_itraq4plex_channel_117_description:
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66 -itraq4plex:channel_117_description "$param_itraq4plex_channel_117_description"
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67 #end if
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68 #if $param_itraq4plex_reference_channel:
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69 -itraq4plex:reference_channel $param_itraq4plex_reference_channel
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70 #end if
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71
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72 #if $rep_param_itraq4plex_correction_matrix:
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73 -itraq4plex:correction_matrix
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74 #for token in $rep_param_itraq4plex_correction_matrix:
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75 #if " " in str(token):
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76 "$token.param_itraq4plex_correction_matrix"
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77 #else
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78 $token.param_itraq4plex_correction_matrix
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79 #end if
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80 #end for
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81 #end if
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82 #if $param_itraq8plex_channel_113_description:
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83 -itraq8plex:channel_113_description "$param_itraq8plex_channel_113_description"
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84 #end if
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85 #if $param_itraq8plex_channel_114_description:
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86 -itraq8plex:channel_114_description "$param_itraq8plex_channel_114_description"
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87 #end if
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88 #if $param_itraq8plex_channel_115_description:
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89 -itraq8plex:channel_115_description "$param_itraq8plex_channel_115_description"
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90 #end if
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91 #if $param_itraq8plex_channel_116_description:
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92 -itraq8plex:channel_116_description "$param_itraq8plex_channel_116_description"
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93 #end if
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94 #if $param_itraq8plex_channel_117_description:
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95 -itraq8plex:channel_117_description "$param_itraq8plex_channel_117_description"
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96 #end if
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97 #if $param_itraq8plex_channel_118_description:
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98 -itraq8plex:channel_118_description "$param_itraq8plex_channel_118_description"
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99 #end if
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100 #if $param_itraq8plex_channel_119_description:
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101 -itraq8plex:channel_119_description "$param_itraq8plex_channel_119_description"
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102 #end if
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103 #if $param_itraq8plex_channel_121_description:
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104 -itraq8plex:channel_121_description "$param_itraq8plex_channel_121_description"
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105 #end if
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106 #if $param_itraq8plex_reference_channel:
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107 -itraq8plex:reference_channel $param_itraq8plex_reference_channel
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108 #end if
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109
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110 #if $rep_param_itraq8plex_correction_matrix:
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111 -itraq8plex:correction_matrix
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112 #for token in $rep_param_itraq8plex_correction_matrix:
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113 #if " " in str(token):
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114 "$token.param_itraq8plex_correction_matrix"
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115 #else
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116 $token.param_itraq8plex_correction_matrix
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117 #end if
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118 #end for
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119 #end if
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120 #if $param_quantification_isotope_correction:
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121 -quantification:isotope_correction
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122 #end if
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123 #if $param_quantification_normalization:
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124 -quantification:normalization
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125 #end if
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126 #if $param_tmt10plex_channel_126_description:
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127 -tmt10plex:channel_126_description "$param_tmt10plex_channel_126_description"
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128 #end if
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129 #if $param_tmt10plex_channel_127N_description:
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130 -tmt10plex:channel_127N_description "$param_tmt10plex_channel_127N_description"
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131 #end if
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132 #if $param_tmt10plex_channel_127C_description:
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133 -tmt10plex:channel_127C_description "$param_tmt10plex_channel_127C_description"
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134 #end if
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135 #if $param_tmt10plex_channel_128N_description:
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136 -tmt10plex:channel_128N_description "$param_tmt10plex_channel_128N_description"
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137 #end if
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138 #if $param_tmt10plex_channel_128C_description:
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139 -tmt10plex:channel_128C_description "$param_tmt10plex_channel_128C_description"
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140 #end if
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141 #if $param_tmt10plex_channel_129N_description:
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142 -tmt10plex:channel_129N_description "$param_tmt10plex_channel_129N_description"
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143 #end if
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144 #if $param_tmt10plex_channel_129C_description:
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145 -tmt10plex:channel_129C_description "$param_tmt10plex_channel_129C_description"
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146 #end if
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147 #if $param_tmt10plex_channel_130N_description:
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148 -tmt10plex:channel_130N_description "$param_tmt10plex_channel_130N_description"
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149 #end if
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150 #if $param_tmt10plex_channel_130C_description:
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151 -tmt10plex:channel_130C_description "$param_tmt10plex_channel_130C_description"
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152 #end if
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153 #if $param_tmt10plex_channel_131_description:
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154 -tmt10plex:channel_131_description "$param_tmt10plex_channel_131_description"
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155 #end if
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156 #if $param_tmt10plex_reference_channel:
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157 -tmt10plex:reference_channel
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158 #if " " in str($param_tmt10plex_reference_channel):
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159 "$param_tmt10plex_reference_channel"
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160 #else
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161 $param_tmt10plex_reference_channel
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162 #end if
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163 #end if
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164
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165 #if $rep_param_tmt10plex_correction_matrix:
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166 -tmt10plex:correction_matrix
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167 #for token in $rep_param_tmt10plex_correction_matrix:
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168 #if " " in str(token):
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169 "$token.param_tmt10plex_correction_matrix"
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170 #else
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171 $token.param_tmt10plex_correction_matrix
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172 #end if
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173 #end for
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174 #end if
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175 #if $param_tmt6plex_channel_126_description:
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176 -tmt6plex:channel_126_description "$param_tmt6plex_channel_126_description"
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177 #end if
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178 #if $param_tmt6plex_channel_127_description:
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179 -tmt6plex:channel_127_description "$param_tmt6plex_channel_127_description"
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180 #end if
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181 #if $param_tmt6plex_channel_128_description:
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182 -tmt6plex:channel_128_description "$param_tmt6plex_channel_128_description"
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183 #end if
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184 #if $param_tmt6plex_channel_129_description:
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185 -tmt6plex:channel_129_description "$param_tmt6plex_channel_129_description"
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186 #end if
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187 #if $param_tmt6plex_channel_130_description:
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188 -tmt6plex:channel_130_description "$param_tmt6plex_channel_130_description"
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189 #end if
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190 #if $param_tmt6plex_channel_131_description:
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191 -tmt6plex:channel_131_description "$param_tmt6plex_channel_131_description"
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192 #end if
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193 #if $param_tmt6plex_reference_channel:
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194 -tmt6plex:reference_channel $param_tmt6plex_reference_channel
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195 #end if
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196
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197 #if $rep_param_tmt6plex_correction_matrix:
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198 -tmt6plex:correction_matrix
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199 #for token in $rep_param_tmt6plex_correction_matrix:
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200 #if " " in str(token):
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201 "$token.param_tmt6plex_correction_matrix"
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202 #else
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203 $token.param_tmt6plex_correction_matrix
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204 #end if
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205 #end for
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206 #end if
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207 #if $adv_opts.adv_opts_selector=='advanced':
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208 #if $adv_opts.param_force:
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209 -force
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210 #end if
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211 #if $adv_opts.param_extraction_precursor_isotope_deviation:
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212 -extraction:precursor_isotope_deviation $adv_opts.param_extraction_precursor_isotope_deviation
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213 #end if
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214 #if $adv_opts.param_extraction_purity_interpolation:
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215 -extraction:purity_interpolation
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216 #end if
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217 #end if
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218 </command>
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219 <inputs>
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220 <param name="param_type" type="select" optional="True" value="itraq4plex" label="Isobaric Quantitation method used in the experiment" help="(-type) ">
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221 <option value="itraq4plex">itraq4plex</option>
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222 <option value="itraq8plex">itraq8plex</option>
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223 <option value="tmt10plex">tmt10plex</option>
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224 <option value="tmt6plex">tmt6plex</option>
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225 </param>
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226 <param name="param_in" type="data" format="mzml" optional="False" label="input raw/picked data file" help="(-in) "/>
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227 <param name="param_id_pool" type="text" size="30" label="ID pool file to DocumentID's for all generated output files" help="(-id_pool) Disabled by default. (Set to 'main' to use /home/thouwaar/Downloads/openms-2.0-Linux-x86_64/share/OpenMS/IDPool/IDPool.txt)">
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228 <sanitizer>
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229 <valid initial="string.printable">
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230 <remove value="'"/>
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231 <remove value="""/>
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232 </valid>
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233 </sanitizer>
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234 </param>
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235 <param name="param_extraction_select_activation" type="select" optional="True" value="High-energy collision-induced dissociation" label="Operate only on MSn scans where any of its precursors features a certain activation method (" help="(-select_activation) e.g., usually HCD for iTRAQ). Set to empty string if you want to disable filtering">
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236 <option value="Collision-induced dissociation">Collision-induced dissociation</option>
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237 <option value="Post-source decay">Post-source decay</option>
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238 <option value="Plasma desorption">Plasma desorption</option>
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239 <option value="Surface-induced dissociation">Surface-induced dissociation</option>
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240 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option>
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241 <option value="Electron capture dissociation">Electron capture dissociation</option>
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242 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option>
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243 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option>
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244 <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option>
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245 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option>
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246 <option value="Photodissociation">Photodissociation</option>
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247 <option value="Electron transfer dissociation">Electron transfer dissociation</option>
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248 <option value=""></option>
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249 </param>
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250 <param name="param_extraction_reporter_mass_shift" type="float" min="1e-08" max="0.5" optional="True" value="0.1" label="Allowed shift (left to right) in Da from the expected position" help="(-reporter_mass_shift) "/>
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251 <param name="param_extraction_min_precursor_intensity" type="float" min="0.0" optional="True" value="1.0" label="Minimum intensity of the precursor to be extracted" help="(-min_precursor_intensity) MS/MS scans having a precursor with a lower intensity will not be considered for quantitation"/>
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252 <param name="param_extraction_keep_unannotated_precursor" type="boolean" truevalue="-extraction:keep_unannotated_precursor" falsevalue="" checked="true" optional="True" label="Flag if precursor with missing intensity value or missing precursor spectrum should be included or not" help="(-keep_unannotated_precursor) "/>
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253 <param name="param_extraction_min_reporter_intensity" type="float" min="0.0" optional="True" value="0.0" label="Minimum intensity of the individual reporter ions to be extracted" help="(-min_reporter_intensity) "/>
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254 <param name="param_extraction_discard_low_intensity_quantifications" type="boolean" truevalue="-extraction:discard_low_intensity_quantifications" falsevalue="" checked="false" optional="True" label="Remove all reporter intensities if a single reporter is below the threshold given in 'min_reporter_intensity'" help="(-discard_low_intensity_quantifications) "/>
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255 <param name="param_extraction_min_precursor_purity" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Minimum fraction of the total intensity in the isolation window of the precursor spectrum attributable to the selected precurso" help="(-min_precursor_purity) "/>
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256 <param name="param_itraq4plex_channel_114_description" type="text" size="30" label="Description for the content of the 114 channel" help="(-channel_114_description) ">
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257 <sanitizer>
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258 <valid initial="string.printable">
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259 <remove value="'"/>
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260 <remove value="""/>
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261 </valid>
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262 </sanitizer>
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263 </param>
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264 <param name="param_itraq4plex_channel_115_description" type="text" size="30" label="Description for the content of the 115 channel" help="(-channel_115_description) ">
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265 <sanitizer>
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266 <valid initial="string.printable">
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267 <remove value="'"/>
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268 <remove value="""/>
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269 </valid>
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270 </sanitizer>
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271 </param>
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272 <param name="param_itraq4plex_channel_116_description" type="text" size="30" label="Description for the content of the 116 channel" help="(-channel_116_description) ">
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273 <sanitizer>
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274 <valid initial="string.printable">
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275 <remove value="'"/>
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276 <remove value="""/>
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277 </valid>
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278 </sanitizer>
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279 </param>
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280 <param name="param_itraq4plex_channel_117_description" type="text" size="30" label="Description for the content of the 117 channel" help="(-channel_117_description) ">
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281 <sanitizer>
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282 <valid initial="string.printable">
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283 <remove value="'"/>
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284 <remove value="""/>
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285 </valid>
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286 </sanitizer>
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287 </param>
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288 <param name="param_itraq4plex_reference_channel" type="integer" min="114" max="117" optional="True" value="114" label="Number of the reference channel (114-117)" help="(-reference_channel) "/>
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289 <repeat name="rep_param_itraq4plex_correction_matrix" min="0" max="1" title="param_itraq4plex_correction_matrix">
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290 <param name="param_itraq4plex_correction_matrix" type="text" size="30" value="0.0/1.0/5.9/0.2 0.0/2.0/5.6/0.1 0.0/3.0/4.5/0.1 0.1/4.0/3.5/0.1" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" help="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'">
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291 <sanitizer>
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292 <valid initial="string.printable">
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293 <remove value="'"/>
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294 <remove value="""/>
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295 </valid>
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296 </sanitizer>
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297 </param>
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298 </repeat>
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299 <param name="param_itraq8plex_channel_113_description" type="text" size="30" label="Description for the content of the 113 channel" help="(-channel_113_description) ">
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300 <sanitizer>
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301 <valid initial="string.printable">
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302 <remove value="'"/>
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303 <remove value="""/>
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304 </valid>
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305 </sanitizer>
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306 </param>
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307 <param name="param_itraq8plex_channel_114_description" type="text" size="30" label="Description for the content of the 114 channel" help="(-channel_114_description) ">
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308 <sanitizer>
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309 <valid initial="string.printable">
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310 <remove value="'"/>
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311 <remove value="""/>
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312 </valid>
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313 </sanitizer>
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314 </param>
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315 <param name="param_itraq8plex_channel_115_description" type="text" size="30" label="Description for the content of the 115 channel" help="(-channel_115_description) ">
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316 <sanitizer>
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317 <valid initial="string.printable">
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318 <remove value="'"/>
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319 <remove value="""/>
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320 </valid>
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321 </sanitizer>
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322 </param>
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323 <param name="param_itraq8plex_channel_116_description" type="text" size="30" label="Description for the content of the 116 channel" help="(-channel_116_description) ">
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324 <sanitizer>
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325 <valid initial="string.printable">
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326 <remove value="'"/>
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327 <remove value="""/>
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328 </valid>
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329 </sanitizer>
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330 </param>
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331 <param name="param_itraq8plex_channel_117_description" type="text" size="30" label="Description for the content of the 117 channel" help="(-channel_117_description) ">
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332 <sanitizer>
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333 <valid initial="string.printable">
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334 <remove value="'"/>
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335 <remove value="""/>
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336 </valid>
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337 </sanitizer>
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338 </param>
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339 <param name="param_itraq8plex_channel_118_description" type="text" size="30" label="Description for the content of the 118 channel" help="(-channel_118_description) ">
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340 <sanitizer>
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341 <valid initial="string.printable">
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342 <remove value="'"/>
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343 <remove value="""/>
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344 </valid>
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345 </sanitizer>
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346 </param>
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347 <param name="param_itraq8plex_channel_119_description" type="text" size="30" label="Description for the content of the 119 channel" help="(-channel_119_description) ">
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348 <sanitizer>
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349 <valid initial="string.printable">
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350 <remove value="'"/>
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351 <remove value="""/>
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352 </valid>
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353 </sanitizer>
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354 </param>
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355 <param name="param_itraq8plex_channel_121_description" type="text" size="30" label="Description for the content of the 121 channel" help="(-channel_121_description) ">
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356 <sanitizer>
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357 <valid initial="string.printable">
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358 <remove value="'"/>
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359 <remove value="""/>
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360 </valid>
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361 </sanitizer>
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362 </param>
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363 <param name="param_itraq8plex_reference_channel" type="integer" min="113" max="121" optional="True" value="113" label="Number of the reference channel (113-121)" help="(-reference_channel) Please note that 120 is not valid"/>
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364 <repeat name="rep_param_itraq8plex_correction_matrix" min="0" max="1" title="param_itraq8plex_correction_matrix">
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365 <param name="param_itraq8plex_correction_matrix" type="text" size="30" value="0.00/0.00/6.89/0.22 0.00/0.94/5.90/0.16 0.00/1.88/4.90/0.10 0.00/2.82/3.90/0.07 0.06/3.77/2.99/0.00 0.09/4.71/1.88/0.00 0.14/5.66/0.87/0.00 0.27/7.44/0.18/0.00" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" help="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'">
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366 <sanitizer>
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367 <valid initial="string.printable">
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368 <remove value="'"/>
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369 <remove value="""/>
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370 </valid>
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371 </sanitizer>
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372 </param>
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373 </repeat>
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374 <param name="param_quantification_isotope_correction" type="boolean" truevalue="-quantification:isotope_correction" falsevalue="" checked="true" optional="True" label="Enable isotope correction (highly recommended)" help="(-isotope_correction) Note that you need to provide a correct isotope correction matrix otherwise the tool will fail or produce invalid results"/>
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375 <param name="param_quantification_normalization" type="boolean" truevalue="-quantification:normalization" falsevalue="" checked="false" optional="True" label="Enable normalization of channel intensities with respect to the reference channel" help="(-normalization) The normalization is done by using the Median of Ratios (every channel / Reference). Also the ratio of medians (from any channel and reference) is provided as control measure!"/>
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376 <param name="param_tmt10plex_channel_126_description" type="text" size="30" label="Description for the content of the 126 channel" help="(-channel_126_description) ">
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377 <sanitizer>
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378 <valid initial="string.printable">
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379 <remove value="'"/>
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380 <remove value="""/>
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381 </valid>
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382 </sanitizer>
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383 </param>
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384 <param name="param_tmt10plex_channel_127N_description" type="text" size="30" label="Description for the content of the 127N channel" help="(-channel_127N_description) ">
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385 <sanitizer>
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386 <valid initial="string.printable">
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387 <remove value="'"/>
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388 <remove value="""/>
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389 </valid>
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390 </sanitizer>
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391 </param>
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392 <param name="param_tmt10plex_channel_127C_description" type="text" size="30" label="Description for the content of the 127C channel" help="(-channel_127C_description) ">
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393 <sanitizer>
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394 <valid initial="string.printable">
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395 <remove value="'"/>
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396 <remove value="""/>
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397 </valid>
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398 </sanitizer>
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399 </param>
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400 <param name="param_tmt10plex_channel_128N_description" type="text" size="30" label="Description for the content of the 128N channel" help="(-channel_128N_description) ">
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401 <sanitizer>
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402 <valid initial="string.printable">
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403 <remove value="'"/>
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404 <remove value="""/>
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405 </valid>
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406 </sanitizer>
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407 </param>
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408 <param name="param_tmt10plex_channel_128C_description" type="text" size="30" label="Description for the content of the 128C channel" help="(-channel_128C_description) ">
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409 <sanitizer>
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410 <valid initial="string.printable">
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411 <remove value="'"/>
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412 <remove value="""/>
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413 </valid>
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414 </sanitizer>
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415 </param>
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416 <param name="param_tmt10plex_channel_129N_description" type="text" size="30" label="Description for the content of the 129N channel" help="(-channel_129N_description) ">
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417 <sanitizer>
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418 <valid initial="string.printable">
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419 <remove value="'"/>
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420 <remove value="""/>
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421 </valid>
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422 </sanitizer>
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423 </param>
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424 <param name="param_tmt10plex_channel_129C_description" type="text" size="30" label="Description for the content of the 129C channel" help="(-channel_129C_description) ">
|
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425 <sanitizer>
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426 <valid initial="string.printable">
|
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427 <remove value="'"/>
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428 <remove value="""/>
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429 </valid>
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430 </sanitizer>
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431 </param>
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432 <param name="param_tmt10plex_channel_130N_description" type="text" size="30" label="Description for the content of the 130N channel" help="(-channel_130N_description) ">
|
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433 <sanitizer>
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434 <valid initial="string.printable">
|
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435 <remove value="'"/>
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436 <remove value="""/>
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437 </valid>
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438 </sanitizer>
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439 </param>
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440 <param name="param_tmt10plex_channel_130C_description" type="text" size="30" label="Description for the content of the 130C channel" help="(-channel_130C_description) ">
|
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441 <sanitizer>
|
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|
442 <valid initial="string.printable">
|
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443 <remove value="'"/>
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444 <remove value="""/>
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445 </valid>
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446 </sanitizer>
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447 </param>
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448 <param name="param_tmt10plex_channel_131_description" type="text" size="30" label="Description for the content of the 131 channel" help="(-channel_131_description) ">
|
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449 <sanitizer>
|
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|
450 <valid initial="string.printable">
|
|
|
451 <remove value="'"/>
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452 <remove value="""/>
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453 </valid>
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|
454 </sanitizer>
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455 </param>
|
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456 <param name="param_tmt10plex_reference_channel" type="select" optional="True" value="126" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131)" help="(-reference_channel) ">
|
|
|
457 <option value="126">126</option>
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|
|
458 <option value="127N">127N</option>
|
|
|
459 <option value="127C">127C</option>
|
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460 <option value="128N">128N</option>
|
|
|
461 <option value="128C">128C</option>
|
|
|
462 <option value="129N">129N</option>
|
|
|
463 <option value="129C">129C</option>
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|
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464 <option value="130N">130N</option>
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|
|
465 <option value="130C">130C</option>
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466 <option value="131">131</option>
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|
|
467 </param>
|
|
|
468 <repeat name="rep_param_tmt10plex_correction_matrix" min="0" max="1" title="param_tmt10plex_correction_matrix">
|
|
|
469 <param name="param_tmt10plex_correction_matrix" type="text" size="30" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" help="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'">
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|
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470 <sanitizer>
|
|
|
471 <valid initial="string.printable">
|
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472 <remove value="'"/>
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473 <remove value="""/>
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474 </valid>
|
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475 </sanitizer>
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476 </param>
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477 </repeat>
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|
478 <param name="param_tmt6plex_channel_126_description" type="text" size="30" label="Description for the content of the 126 channel" help="(-channel_126_description) ">
|
|
|
479 <sanitizer>
|
|
|
480 <valid initial="string.printable">
|
|
|
481 <remove value="'"/>
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482 <remove value="""/>
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483 </valid>
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484 </sanitizer>
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485 </param>
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486 <param name="param_tmt6plex_channel_127_description" type="text" size="30" label="Description for the content of the 127 channel" help="(-channel_127_description) ">
|
|
|
487 <sanitizer>
|
|
|
488 <valid initial="string.printable">
|
|
|
489 <remove value="'"/>
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|
490 <remove value="""/>
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|
491 </valid>
|
|
|
492 </sanitizer>
|
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|
493 </param>
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494 <param name="param_tmt6plex_channel_128_description" type="text" size="30" label="Description for the content of the 128 channel" help="(-channel_128_description) ">
|
|
|
495 <sanitizer>
|
|
|
496 <valid initial="string.printable">
|
|
|
497 <remove value="'"/>
|
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|
498 <remove value="""/>
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|
|
499 </valid>
|
|
|
500 </sanitizer>
|
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|
501 </param>
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|
502 <param name="param_tmt6plex_channel_129_description" type="text" size="30" label="Description for the content of the 129 channel" help="(-channel_129_description) ">
|
|
|
503 <sanitizer>
|
|
|
504 <valid initial="string.printable">
|
|
|
505 <remove value="'"/>
|
|
|
506 <remove value="""/>
|
|
|
507 </valid>
|
|
|
508 </sanitizer>
|
|
|
509 </param>
|
|
|
510 <param name="param_tmt6plex_channel_130_description" type="text" size="30" label="Description for the content of the 130 channel" help="(-channel_130_description) ">
|
|
|
511 <sanitizer>
|
|
|
512 <valid initial="string.printable">
|
|
|
513 <remove value="'"/>
|
|
|
514 <remove value="""/>
|
|
|
515 </valid>
|
|
|
516 </sanitizer>
|
|
|
517 </param>
|
|
|
518 <param name="param_tmt6plex_channel_131_description" type="text" size="30" label="Description for the content of the 131 channel" help="(-channel_131_description) ">
|
|
|
519 <sanitizer>
|
|
|
520 <valid initial="string.printable">
|
|
|
521 <remove value="'"/>
|
|
|
522 <remove value="""/>
|
|
|
523 </valid>
|
|
|
524 </sanitizer>
|
|
|
525 </param>
|
|
|
526 <param name="param_tmt6plex_reference_channel" type="integer" min="126" max="131" optional="True" value="126" label="Number of the reference channel (126-131)" help="(-reference_channel) "/>
|
|
|
527 <repeat name="rep_param_tmt6plex_correction_matrix" min="0" max="1" title="param_tmt6plex_correction_matrix">
|
|
|
528 <param name="param_tmt6plex_correction_matrix" type="text" size="30" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: <-2Da>/<-1Da>/<+1Da>/<+2Da>;" help="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'">
|
|
|
529 <sanitizer>
|
|
|
530 <valid initial="string.printable">
|
|
|
531 <remove value="'"/>
|
|
|
532 <remove value="""/>
|
|
|
533 </valid>
|
|
|
534 </sanitizer>
|
|
|
535 </param>
|
|
|
536 </repeat>
|
|
|
537 <expand macro="advanced_options">
|
|
|
538 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
|
|
|
539 <param name="param_extraction_precursor_isotope_deviation" type="float" min="0.0" optional="True" value="10.0" label="Maximum allowed deviation (in ppm) between theoretical and observed isotopic peaks of the precursor peak in the isolation window to be counted as part of the precurso" help="(-precursor_isotope_deviation) "/>
|
|
|
540 <param name="param_extraction_purity_interpolation" type="boolean" truevalue="-extraction:purity_interpolation" falsevalue="" checked="true" optional="True" label="If set to true the algorithm will try to compute the purity as a time weighted linear combination of the precursor scan and the following scan" help="(-purity_interpolation) If set to false, only the precursor scan will be used"/>
|
|
|
541 </expand>
|
|
|
542 </inputs>
|
|
|
543 <outputs>
|
|
|
544 <data name="param_out" format="consensusxml"/>
|
|
|
545 </outputs>
|
|
|
546 <help>**What it does**
|
|
|
547
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|
|
548 Calculates isobaric quantitative values for peptides
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|
|
549
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|
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550
|
|
|
551 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IsobaricAnalyzer.html</help>
|
|
|
552 <expand macro="references"/>
|
|
|
553 </tool>
|
