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