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1 <tool id="nist_wrapper" name="NIST MSSEARCH" version="0.0.1">
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2 <!--
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3 This part is a WORKAROUND for the wine X11 dependency, allowing it to run headless :
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4 -> install Xvfb and enable it on a port, say 995:
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5 -> make sure this gets executed: export DISPLAY=:995;
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6 -->
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7 <description> Runs NIST's msseach program to match spectra against metabolite libraries</description>
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2
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8
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9 <requirements>
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10 <requirement name="package" version="0.2">nist_wrapper_venv</requirement>
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11 </requirements>
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12
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0
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13 <command interpreter="export DISPLAY=:0; python">
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14 nist_wrapper.py
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15 "~/.wine/drive_c/NIST"
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16 $nistIniFile
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17 $spectraFile
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18 $outputFile
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19 </command>
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20 <inputs>
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21 <param name="spectraFile" type="data" format="msp" label="Spectra file (.MSP)" help="E.g. file produced by MsClust"/>
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22
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23 <param name="hitsToReport" type="integer" size="10" value="3" label="Number of matches to report per spetrum"
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24 help="Top X matches for each spectrum will be written to output file." />
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25
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26 </inputs>
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27 <configfiles>
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28
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29 <configfile name="nistIniFile">[MAIN]
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30 Version=2.0
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31 Library Directory=C:\NISTDEMO\MSSEARCH\
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32 Program=NIST MS
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33 Active Frame=0
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34 Placement_flags=2
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35 Placement_show=3
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36 Placement_minx=-32000
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37 Placement_miny=-32000
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38 Placement_maxx=-1
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39 Placement_maxy=-1
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40 Placement_left=0
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41 Placement_top=84
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42 Placement_right=1440
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43 Placement_bottom=827
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44 Wrong Libraries=
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45 Active Show=3
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46 Display Warning=1
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47 Display Info=0
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48 [Search Options]
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49 Automatic=1
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50 Type=1
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51 As MW=1
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52 MW=1
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53 Reverse=0
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54 Penalize=0
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55 Search with MW=1
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56 Preasearch=0
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57 Apply Limits=0
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58 Min Mass Type=0
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59 Min Mass=1
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60 Max Mass ON=0
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61 Max Mass=2000
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62 Min Abund ON=0
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63 Min Abund=1
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64 Printing=0
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65 Return Focus=0
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66 Hits to Print=${hitsToReport}
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67 Print Spectra=1
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68 Print Structure=1
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69 Apply MaxLength=0
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70 MaxLength=2000
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71 Sort Mode=0
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72 Match Clusters=1
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73 Match Rings=1
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74 Weighting=0
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75 Use Specified Parent=0
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76 Ignore Precursor=0
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77 Parent Mass=0
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78 Precursor Tolerance=1.6
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79 Ions Tolerance=0.8
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80 [Libraries]
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81 Library_0=mainlib
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82 Library_1=
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83 Library_2=
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84 Library_3=
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85 Library_4=
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86 Library_5=
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87 Library_6=
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88 Library_7=
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89 Library_8=
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90 Library_9=
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91 Library_10=
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92 Library_11=
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93 Library_12=
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94 Library_13=
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95 Library_14=
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96 Library_15=
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97 Order_0=1 1
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98 Order_1=1 1
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99 Order_2=1 1
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100 Order_3=1 1
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101 Order_4=1 1
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102 Order_5=1 1
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103 Order_6=1 1
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104 Order_7=1 1
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105 Order_8=1 1
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106 Order_9=1 1
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107 [ICHI]
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108 On=1
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109 Isotope=1
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110 Stereo=0
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111 Derivative=1
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112 [Import]
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113 Dir=C:\NISTDEMO\MSSEARCH\
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114 Synonyms=1
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115 Filter=1
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116 Coeff=1 0
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117 [Structure Import]
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118 Dir=C:\NISTDEMO\MSSEARCH\
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119 Filter=1
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120 [Export]
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121 Dir=C:\NISTDEMO\MSSEARCH\
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122 Synonyms=1
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123 Filter=1
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124 Coeff=1 0
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125 [Search Options]
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126 Automatic=1
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127 [Library Search]
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128 SpecList Tab=1
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129 Placement_flags=2
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130 Placement_show=3
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131 ;Layout=1
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132 ;Hit Splitter Orientation=1
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133 ;List Tab=0
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134 ;Compare Tab=0
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135 ;Hit Tab=0
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136 ;Unknown Tab=0
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137 Placement_minx=-1
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138 Placement_miny=-1
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139 ;Placement_maxx=-4
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140 Placement_maxx=-8
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141 ;Placement_maxy=-23
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142 Placement_maxy=-30
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143 Placement_left=0
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144 Placement_top=1
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145 Placement_right=678
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146 Placement_bottom=397
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147 Splitter=0.314139
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148 List Splitter=0 0
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149 Unknown Splitter=0.493119
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150 Unknown Splitter Orientation=1
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151 ;Compare Splitter=0.3333 0.3333
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152 Compare Splitter=0 0
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153 Hit Splitter=0.493874
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154 SpecList Splitter=0.493119
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155 SpecList Splitter Orientation=1
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156 Hits Column=10 41 39 58 68 56 256 0 0 0 0
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157 ;SpecList Column=3 41 41 56
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158 ;SpecList Column=3 41 41 156
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159 SpecList Column=10 41 38 128 0 0 48 0 0 0 0
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160 Layout=1
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161 Hit Splitter Orientation=1
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162 List Tab=0
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163 Compare Tab=0
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164 Hit Tab=0
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165 Unknown Tab=0
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166 Replicates=0
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167 Exact Match=0
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168 [BAR-Summary]
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169 Bars=4
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170 ScreenCX=1600
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171 ScreenCY=900
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172 [REPORT]
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173 Ten Largest Peaks=1
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174 Compound Info=1
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175 Mass Intensity List=0
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176 Synonyms=1
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177 Plot=1
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178 Structure=1
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179 First Hits=1
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180 First Hits Number=3
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181 Unknown=0
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182 [Substructure Export]
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183 Filter=1
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184 Dir=
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185 [Substructure Import]
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186 Filter=1
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187 Dir=
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188 [Search AnyPeaks Options]
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189 Other=0
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190 Peaks=0
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191 Hitlist size=100
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192 Peak0=
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193 Peak1=
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194 Peak2=
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195 Peak3=
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196 Peak4=
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197 Peak5=
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198 Peak6=
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199 Peak7=
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200 Peak8=
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201 Peak9=
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202 Peak10=
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203 [Other Searches Options]
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204 CAS=
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205 MW=1
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206 ID=
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207 EPA=
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208 Formula=
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209 Seq Hitlist size=100
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210 [Constraints]
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211 Library ON=0
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212 Formula ON=0
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213 MW ON=0
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214 AnyPeaks ON=0
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215 Sequentiial ON=0
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216 Active MW=0
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217 MINMW=1
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218 MAXMW=2000
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219 Active Name=0
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220 Name Fragment=
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221 Elements Value=0
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222 Elements Present=0
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223 Mode Elements=0
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224 Num Elements=0
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225 Elements0=
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226 Elements1=
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227 Elements2=
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228 Elements3=
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229 Elements4=
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230 Elements5=
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231 Elements6=
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232 Elements7=
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233 Elements8=
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234 Elements9=
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235 Num Compare Elements=0
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236 Compare Elements0=
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237 Compare Elements1=
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238 Compare Elements2=
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239 Compare Elements3=
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240 Compare Elements4=
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241 Compare Elements5=
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242 Compare Elements6=
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243 Compare Elements7=
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244 Compare Elements8=
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245 Compare Elements9=
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246 Active Peaks=0
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247 Mode Peaks=1
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248 Num AnyPeaks=0
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249 Active OtherDB=0
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250 OtherDB=0
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251 Active Tags=0
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252 Tags=
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253 Active Peptide Sequence=0
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254 Peptide Sequence=
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255 Active Proton=0
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256 Proton Mode=0
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257 Proton Low=
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258 Proton Hi=
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259 Proton Exact=
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260 Active Charge=0
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261 Charge Mode=0
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262 Charge Low=
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263 Charge Hi=
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264 Charge Exact=
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265 Active Residue=0
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266 Residue Mode=0
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267 Residue Low=
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268 Residue Hi=
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269 Residue Exact=
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270 [Peptide Search Options]
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271 Cysteine Modification=0
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272 Comment Fields=
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273 Show Fields On Plot=1
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274 TF qry=0
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275 E Omssa=0
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276 TF lib=0
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277 RevImp=0
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278 Weight Omssa=0
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279 Weight Num Rep=0
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280 Weight Qtof=0
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281 Treshold=0
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282 [Library Hit]
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283 Font Name=MS Shell Dlg
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284 Font Pts=-8
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285 Font Width=0
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286 Font Esc=0
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287 Font Orientation=0
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288 Font Weight=400
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289 Font IUSC=0
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290 Font PCQP=654311424
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291 Color=0 255 16711680 16777215 16777215 0
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292 Order Number=1
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293 Structure Only=0
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294 Library=0
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295 Structure Size=50
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296 Match=1
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297 Probability=1
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298 Reverse Match=1
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299 Clear History=0
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300 [Library Spec List]
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301 Font Name=MS Shell Dlg
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302 Font Pts=-8
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303 Font Width=0
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304 Font Esc=0
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305 Font Orientation=0
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306 Font Weight=400
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307 Font IUSC=0
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308 Font PCQP=654311424
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309 Color=0 255 16711680 16777215 16777215 0
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310 Order Number=1
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311 Structure Only=0
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312 Library=0
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313 Structure Size=50
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314 Match=0
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315 Probability=0
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316 Reverse Match=0
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317 Clear History=0
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318 [Library Unknown Plot]
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319 Font Name=MS Shell Dlg
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320 Font Pts=-8
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321 Font Width=0
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322 Font Esc=0
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323 Font Orientation=0
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324 Font Weight=400
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325 Font IUSC=0
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326 Font PCQP=654311424
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327 Color=0 255 16711680 0 255 16777215
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328 Limits ON=0
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329 Wrap=0
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330 MW=0
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331 CAS=0
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332 Formula=0
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333 Threshold=0
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334 Structure=1
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335 Width=1
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336 Mass Label=1
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337 Pep Label=0
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338 [Library Hit Plot]
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339 Font Name=MS Shell Dlg
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340 Font Pts=-8
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341 Font Width=0
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342 Font Esc=0
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343 Font Orientation=0
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344 Font Weight=400
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345 Font IUSC=0
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346 Font PCQP=654311424
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347 Color=0 255 16711680 0 255 16777215
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348 Limits ON=0
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349 Wrap=0
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350 MW=1
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351 CAS=0
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352 Formula=1
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353 Threshold=0
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354 Structure=1
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355 Width=1
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356 Mass Label=1
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357 Pep Label=0
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358 [Library SpecList Plot]
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359 Font Name=MS Shell Dlg
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360 Font Pts=-8
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361 Font Width=0
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362 Font Esc=0
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363 Font Orientation=0
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364 Font Weight=400
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365 Font IUSC=0
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366 Font PCQP=654311424
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367 Color=0 255 16711680 0 255 16777215
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368 Limits ON=0
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369 Wrap=0
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370 MW=0
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371 CAS=0
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372 Formula=0
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373 Threshold=0
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374 Structure=1
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375 Width=1
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376 Mass Label=1
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377 Pep Label=0
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378 [Library Unknown Text]
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379 Font Name=MS Shell Dlg
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380 Font Pts=-8
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381 Font Width=0
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382 Font Esc=0
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383 Font Orientation=0
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384 Font Weight=400
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385 Font IUSC=0
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386 Font PCQP=654311424
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387 Color=16711680 0 255 8421376 16777215
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388 Ten Peaks=1
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389 Compound=1
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390 Intensity=0
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391 Synonyms=1
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392 Rows=0
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393 Noise=0
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394 Wrap Synonyms=0
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395 RI=1
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396 RI All=1
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397 RI Num=2
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398 [Library Hit Text]
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399 Font Name=MS Shell Dlg
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400 Font Pts=-8
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401 Font Width=0
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402 Font Esc=0
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403 Font Orientation=0
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404 Font Weight=400
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405 Font IUSC=0
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406 Font PCQP=654311424
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407 Color=16711680 0 255 8421376 16777215
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408 Ten Peaks=1
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409 Compound=1
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410 Intensity=1
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411 Synonyms=1
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412 Rows=0
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413 Noise=0
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414 Wrap Synonyms=0
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415 RI=1
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416 RI All=1
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417 RI Num=2
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418 [Library SpecList Text]
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419 Font Name=MS Shell Dlg
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420 Font Pts=-8
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421 Font Width=0
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422 Font Esc=0
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423 Font Orientation=0
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424 Font Weight=400
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425 Font IUSC=0
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426 Font PCQP=654311424
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427 Color=16711680 0 255 8421376 16777215
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428 Ten Peaks=1
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429 Compound=1
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430 Intensity=0
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431 Synonyms=1
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432 Rows=0
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433 Noise=0
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434 Wrap Synonyms=0
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435 RI=1
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436 RI All=1
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437 RI Num=2
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438 [Library Compare]
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439 Font Name=MS Shell Dlg
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440 Font Pts=-8
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441 Font Width=0
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442 Font Esc=0
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443 Font Orientation=0
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444 Font Weight=400
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445 Font IUSC=0
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446 Font PCQP=654311424
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447 Color=0 255 16711680 32768 16777215
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448 Limit ON=0
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449 Threshold=0
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450 Show=1
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451 Show Structure=0
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452 Independent Zoom=0
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453 Width=1
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454 [Library Histogram]
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455 Font Name=MS Shell Dlg
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456 Font Pts=-8
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457 Font Width=0
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458 Font Esc=0
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459 Font Orientation=0
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460 Font Weight=400
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461 Font IUSC=0
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462 Font PCQP=654311424
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463 Color=0 16711680 255 16777215
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464 Discret=25
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465 Axis=1
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466 Automatic=1
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467 Min=0
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468 Max=1000
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469 [Library Display]
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470 Neutral Loss=0
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471 Scale=0
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472 Min mz=0
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473 Max mz=1000
|
|
|
474 Default Search Anchor=1
|
|
|
475 Search Anchor=0
|
|
|
476 Default Hit Anchor=1
|
|
|
477 Hit Anchor=0
|
|
|
478 Max Loss=70
|
|
|
479 mz=10
|
|
|
480 [Incremental Search]
|
|
|
481 Placement_flags=0
|
|
|
482 Placement_show=1
|
|
|
483 Placement_minx=-1
|
|
|
484 Placement_miny=-1
|
|
|
485 Placement_maxx=-8
|
|
|
486 Placement_maxy=-30
|
|
|
487 Placement_left=50
|
|
|
488 Placement_top=50
|
|
|
489 Placement_right=1269
|
|
|
490 Placement_bottom=449
|
|
|
491 Key=10METHOXYDESERPID
|
|
|
492 Splitter=0.333054
|
|
|
493 Layout=1
|
|
|
494 Plot Splitter=0.5
|
|
|
495 Plot Splitter Orientation=0
|
|
|
496 List Tab=0
|
|
|
497 Spectrum Tab=0
|
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|
498 Alpha=0
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|
499 [Incremental View]
|
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|
500 Font Name=MS Shell Dlg
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|
501 Font Pts=-8
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502 Font Width=0
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503 Font Esc=0
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504 Font Orientation=0
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505 Font Weight=400
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506 Font IUSC=0
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507 Font PCQP=654311424
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508 Color=0 255 16711680 16777215 16777215 0
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|
|
509 Auto Display=1
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|
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510 Structure Only=50
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|
|
511 [Incremental Plot]
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|
512 Font Name=MS Shell Dlg
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|
513 Font Pts=-8
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514 Font Width=0
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515 Font Esc=0
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516 Font Orientation=0
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517 Font Weight=400
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518 Font IUSC=0
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519 Font PCQP=654311424
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520 Color=0 255 16711680 0 255 16777215
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521 Limits ON=0
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522 Wrap=0
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|
523 MW=0
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|
|
524 CAS=0
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|
|
525 Formula=0
|
|
|
526 Threshold=0
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|
|
527 Structure=1
|
|
|
528 Width=1
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|
529 Mass Label=1
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530 Pep Label=0
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531 [Incremental Text]
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532 Font Name=MS Shell Dlg
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533 Font Pts=-8
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534 Font Width=0
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535 Font Esc=0
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536 Font Orientation=0
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537 Font Weight=400
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538 Font IUSC=0
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539 Font PCQP=654311424
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540 Color=16711680 0 255 8421376 16777215
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541 Ten Peaks=1
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542 Compound=1
|
|
|
543 Intensity=0
|
|
|
544 Synonyms=1
|
|
|
545 Rows=0
|
|
|
546 Noise=0
|
|
|
547 Wrap Synonyms=0
|
|
|
548 RI=1
|
|
|
549 RI All=1
|
|
|
550 RI Num=2
|
|
|
551 [Other Search]
|
|
|
552 Placement_flags=0
|
|
|
553 Placement_show=1
|
|
|
554 Placement_minx=-1
|
|
|
555 Placement_miny=-1
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|
|
556 Placement_maxx=-8
|
|
|
557 Placement_maxy=-30
|
|
|
558 Placement_left=25
|
|
|
559 Placement_top=25
|
|
|
560 Placement_right=1244
|
|
|
561 Placement_bottom=424
|
|
|
562 Splitter=0.332215
|
|
|
563 Layout=1
|
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|
564 Plot Splitter=0.5
|
|
|
565 Plot Splitter Orientation=0
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|
566 List Tab=0
|
|
|
567 Spectrum Tab=0
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|
|
568 Replicates=0
|
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569 Search Mode=2
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570 Column=10 39 37 0 0 0 48 0 0 0 0
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571 [Other Hit]
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572 Font Name=MS Shell Dlg
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573 Font Pts=-8
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574 Font Width=0
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575 Font Esc=0
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576 Font Orientation=0
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577 Font Weight=400
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578 Font IUSC=0
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579 Font PCQP=654311424
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580 Color=0 255 16711680 16777215 16777215 0
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581 Order Number=1
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582 Structure Only=0
|
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|
583 Library=0
|
|
|
584 Structure Size=50
|
|
|
585 Match=0
|
|
|
586 Probability=0
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587 Reverse Match=0
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588 Clear History=0
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589 [Other Plot]
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590 Font Name=MS Shell Dlg
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591 Font Pts=-8
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592 Font Width=0
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593 Font Esc=0
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594 Font Orientation=0
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595 Font Weight=400
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596 Font IUSC=0
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597 Font PCQP=654311424
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598 Color=0 255 16711680 0 255 16777215
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|
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599 Limits ON=0
|
|
|
600 Wrap=0
|
|
|
601 MW=0
|
|
|
602 CAS=0
|
|
|
603 Formula=0
|
|
|
604 Threshold=0
|
|
|
605 Structure=1
|
|
|
606 Width=1
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|
|
607 Mass Label=1
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|
608 Pep Label=0
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609 [Other Text]
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|
610 Font Name=MS Shell Dlg
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|
611 Font Pts=-8
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612 Font Width=0
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613 Font Esc=0
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614 Font Orientation=0
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615 Font Weight=400
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616 Font IUSC=0
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617 Font PCQP=654311424
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618 Color=16711680 0 255 8421376 16777215
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|
|
619 Ten Peaks=1
|
|
|
620 Compound=1
|
|
|
621 Intensity=0
|
|
|
622 Synonyms=1
|
|
|
623 Rows=0
|
|
|
624 Noise=0
|
|
|
625 Wrap Synonyms=0
|
|
|
626 RI=1
|
|
|
627 RI All=1
|
|
|
628 RI Num=2
|
|
|
629 [Compare]
|
|
|
630 Placement_flags=0
|
|
|
631 Placement_show=1
|
|
|
632 Placement_minx=-1
|
|
|
633 Placement_miny=-1
|
|
|
634 Placement_maxx=-8
|
|
|
635 Placement_maxy=-30
|
|
|
636 Placement_left=75
|
|
|
637 Placement_top=75
|
|
|
638 Placement_right=1294
|
|
|
639 Placement_bottom=474
|
|
|
640 Splitter=0.244898 0.244898
|
|
|
641 Tab=0
|
|
|
642 [Compare Plot]
|
|
|
643 Font Name=MS Shell Dlg
|
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|
644 Font Pts=-8
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645 Font Width=0
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646 Font Esc=0
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647 Font Orientation=0
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648 Font Weight=400
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649 Font IUSC=0
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|
650 Font PCQP=654311424
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651 Color=0 255 16711680 0 255 16777215
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|
652 Limits ON=0
|
|
|
653 Wrap=0
|
|
|
654 MW=0
|
|
|
655 CAS=0
|
|
|
656 Formula=0
|
|
|
657 Threshold=0
|
|
|
658 Structure=1
|
|
|
659 Width=1
|
|
|
660 Mass Label=1
|
|
|
661 Pep Label=0
|
|
|
662 [Compare Result]
|
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|
663 Font Name=MS Shell Dlg
|
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|
664 Font Pts=-8
|
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665 Font Width=0
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666 Font Esc=0
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667 Font Orientation=0
|
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668 Font Weight=400
|
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669 Font IUSC=0
|
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|
670 Font PCQP=654311424
|
|
|
671 Color=0 255 16711680 32768 16777215
|
|
|
672 Limit ON=0
|
|
|
673 Threshold=0
|
|
|
674 Show=1
|
|
|
675 Show Structure=0
|
|
|
676 Independent Zoom=0
|
|
|
677 Width=1
|
|
|
678 [Compare List]
|
|
|
679 Font Name=MS Shell Dlg
|
|
|
680 Font Pts=-8
|
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|
681 Font Width=0
|
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682 Font Esc=0
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683 Font Orientation=0
|
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|
684 Font Weight=400
|
|
|
685 Font IUSC=0
|
|
|
686 Font PCQP=654311424
|
|
|
687 Color=32768 0 255 16711680 16777215 0 255
|
|
|
688 Names=1
|
|
|
689 No Structure=0
|
|
|
690 Limits ON=0
|
|
|
691 Threshold=0
|
|
|
692 Spectra on Page=3
|
|
|
693 Overwrite=1
|
|
|
694 Insert=1
|
|
|
695 Hits=3
|
|
|
696 Wrap=0
|
|
|
697 MW=0
|
|
|
698 CAS=0
|
|
|
699 Formula=0
|
|
|
700 Width=1
|
|
|
701 Mass Label=1
|
|
|
702 Pep Label=0
|
|
|
703 [Compare Display]
|
|
|
704 Neutral Loss=0
|
|
|
705 Scale=0
|
|
|
706 Min mz=0
|
|
|
707 Max mz=1000
|
|
|
708 Default Search Anchor=1
|
|
|
709 Search Anchor=0
|
|
|
710 Default Hit Anchor=1
|
|
|
711 Hit Anchor=0
|
|
|
712 Max Loss=70
|
|
|
713 mz=10
|
|
|
714 [SpecList]
|
|
|
715 Placement_flags=0
|
|
|
716 Placement_show=1
|
|
|
717 Placement_minx=-1
|
|
|
718 Placement_miny=-1
|
|
|
719 Placement_maxx=-8
|
|
|
720 Placement_maxy=-30
|
|
|
721 Placement_left=100
|
|
|
722 Placement_top=100
|
|
|
723 Placement_right=1319
|
|
|
724 Placement_bottom=499
|
|
|
725 Splitter=0.333054
|
|
|
726 Layout=1
|
|
|
727 Plot Splitter=0.5
|
|
|
728 Plot Splitter Orientation=0
|
|
|
729 List Tab=0
|
|
|
730 Spectrum Tab=0
|
|
|
731 Column=10 39 39 0 0 0 48 0 0 0 0
|
|
|
732 [SpecList Hit]
|
|
|
733 Font Name=MS Shell Dlg
|
|
|
734 Font Pts=-8
|
|
|
735 Font Width=0
|
|
|
736 Font Esc=0
|
|
|
737 Font Orientation=0
|
|
|
738 Font Weight=400
|
|
|
739 Font IUSC=0
|
|
|
740 Font PCQP=654311424
|
|
|
741 Color=0 255 16711680 16777215 16777215 0
|
|
|
742 Order Number=1
|
|
|
743 Structure Only=0
|
|
|
744 Library=0
|
|
|
745 Structure Size=50
|
|
|
746 Match=0
|
|
|
747 Probability=0
|
|
|
748 Reverse Match=0
|
|
|
749 Clear History=0
|
|
|
750 [SpecList Plot]
|
|
|
751 Font Name=MS Shell Dlg
|
|
|
752 Font Pts=-8
|
|
|
753 Font Width=0
|
|
|
754 Font Esc=0
|
|
|
755 Font Orientation=0
|
|
|
756 Font Weight=400
|
|
|
757 Font IUSC=0
|
|
|
758 Font PCQP=654311424
|
|
|
759 Color=0 255 16711680 0 255 16777215
|
|
|
760 Limits ON=0
|
|
|
761 Wrap=0
|
|
|
762 MW=0
|
|
|
763 CAS=0
|
|
|
764 Formula=0
|
|
|
765 Threshold=0
|
|
|
766 Structure=1
|
|
|
767 Width=1
|
|
|
768 Mass Label=1
|
|
|
769 Pep Label=0
|
|
|
770 [SpecList Text]
|
|
|
771 Font Name=MS Shell Dlg
|
|
|
772 Font Pts=-8
|
|
|
773 Font Width=0
|
|
|
774 Font Esc=0
|
|
|
775 Font Orientation=0
|
|
|
776 Font Weight=400
|
|
|
777 Font IUSC=0
|
|
|
778 Font PCQP=654311424
|
|
|
779 Color=16711680 0 255 8421376 16777215
|
|
|
780 Ten Peaks=1
|
|
|
781 Compound=1
|
|
|
782 Intensity=0
|
|
|
783 Synonyms=1
|
|
|
784 Rows=0
|
|
|
785 Noise=0
|
|
|
786 Wrap Synonyms=0
|
|
|
787 RI=1
|
|
|
788 RI All=1
|
|
|
789 RI Num=2
|
|
|
790 [BAR-Bar0]
|
|
|
791 BarID=59419
|
|
|
792 Bars=5
|
|
|
793 Bar#0=0
|
|
|
794 Bar#1=59647
|
|
|
795 Bar#2=0
|
|
|
796 Bar#3=59392
|
|
|
797 Bar#4=0
|
|
|
798 [BAR-Bar1]
|
|
|
799 BarID=59393
|
|
|
800 MRUWidth=0
|
|
|
801 [BAR-Bar2]
|
|
|
802 BarID=59647
|
|
|
803 MRUWidth=288
|
|
|
804 Docking=1
|
|
|
805 MRUDockID=0
|
|
|
806 MRUDockLeftPos=-1
|
|
|
807 MRUDockTopPos=-1
|
|
|
808 MRUDockRightPos=1599
|
|
|
809 MRUDockBottomPos=28
|
|
|
810 MRUFloatStyle=8196
|
|
|
811 MRUFloatXPos=-2147483648
|
|
|
812 MRUFloatYPos=0
|
|
|
813 [BAR-Bar3]
|
|
|
814 BarID=59392
|
|
|
815 YPos=28
|
|
|
816 MRUWidth=276
|
|
|
817 Docking=1
|
|
|
818 MRUDockID=0
|
|
|
819 MRUDockLeftPos=-1
|
|
|
820 MRUDockTopPos=28
|
|
|
821 MRUDockRightPos=294
|
|
|
822 MRUDockBottomPos=61
|
|
|
823 MRUFloatStyle=8196
|
|
|
824 MRUFloatXPos=-2147483648
|
|
|
825 MRUFloatYPos=0</configfile>
|
|
|
826
|
|
|
827 </configfiles>
|
|
|
828
|
|
|
829 <outputs>
|
|
|
830 <data name="outputFile" format="tabular" label="${tool.name} on ${on_string} - NIST library matches (TSV)"/>
|
|
|
831 <data name="outputLog" format="txt" label="${tool.name} on ${on_string} - LOG" hidden="True"/>
|
|
|
832 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - NIST matches report (HTML)"/>
|
|
|
833 </outputs>
|
|
|
834 <tests>
|
|
|
835 <test>
|
|
|
836 </test>
|
|
|
837 </tests>
|
|
|
838 <help>
|
|
|
839
|
|
|
840 .. class:: infomark
|
|
|
841
|
|
|
842 Runs the process also used by NIST mssearch (see screenshot), executing it in batch mode and returning the produced results
|
|
|
843 file with the library matches found for each input spectrum found in the given spectra file.
|
|
|
844
|
|
|
845 .. image:: $PATH_TO_IMAGES/NIST_mssearch_screenshot.png
|
|
|
846
|
|
|
847
|
|
|
848 .. class:: infomark
|
|
|
849
|
|
|
850 This tool requires a valid NIST folder and respective (licensed) libraries to be present on your server.
|
|
|
851 Check http://chemdata.nist.gov/mass-spc/ms-search/ for more information.
|
|
|
852
|
|
|
853 *References*
|
|
|
854
|
|
|
855 NIST Mass Spectral Search Program (Version 2.2)
|
|
|
856
|
|
|
857 http://chemdata.nist.gov/mass-spc/ms-search/docs/Ver20Man_11.pdf
|
|
|
858
|
|
|
859
|
|
|
860 For additional information, see Stein, S.E. “Optimization and Testing of Mass Spectral Library
|
|
|
861 Search Algorithms for Compound Identification” J. Am. Soc. Mass Spectrom. 1994, 5, 859–865.
|
|
|
862
|
|
|
863 </help>
|
|
|
864 </tool> |
