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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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4
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15 "/home/galaxy/.wine/drive_c/NIST"
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0
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16 $nistIniFile
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17 $spectraFile
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18 $outputFile
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3
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19 $outputFileFinal
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7
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20 $outputLog
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3
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21 $htmlReportFile
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22 $htmlReportFile.files_path
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0
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23 </command>
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24 <inputs>
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25 <param name="spectraFile" type="data" format="msp" label="Spectra file (.MSP)" help="E.g. file produced by MsClust"/>
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26
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27 <param name="hitsToReport" type="integer" size="10" value="3" label="Number of matches to report per spetrum"
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28 help="Top X matches for each spectrum will be written to output file." />
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29
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30 </inputs>
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31 <configfiles>
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32
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33 <configfile name="nistIniFile">[MAIN]
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34 Version=2.0
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35 Library Directory=C:\NISTDEMO\MSSEARCH\
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36 Program=NIST MS
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37 Active Frame=0
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38 Placement_flags=2
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39 Placement_show=3
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40 Placement_minx=-32000
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41 Placement_miny=-32000
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42 Placement_maxx=-1
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43 Placement_maxy=-1
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44 Placement_left=0
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45 Placement_top=84
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46 Placement_right=1440
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47 Placement_bottom=827
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48 Wrong Libraries=
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49 Active Show=3
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50 Display Warning=1
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51 Display Info=0
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52 [Search Options]
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53 Automatic=1
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54 Type=1
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55 As MW=1
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56 MW=1
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57 Reverse=0
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58 Penalize=0
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59 Search with MW=1
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60 Preasearch=0
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61 Apply Limits=0
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62 Min Mass Type=0
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63 Min Mass=1
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64 Max Mass ON=0
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65 Max Mass=2000
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66 Min Abund ON=0
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67 Min Abund=1
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68 Printing=0
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69 Return Focus=0
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70 Hits to Print=${hitsToReport}
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71 Print Spectra=1
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72 Print Structure=1
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73 Apply MaxLength=0
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74 MaxLength=2000
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75 Sort Mode=0
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76 Match Clusters=1
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77 Match Rings=1
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78 Weighting=0
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79 Use Specified Parent=0
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80 Ignore Precursor=0
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81 Parent Mass=0
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82 Precursor Tolerance=1.6
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83 Ions Tolerance=0.8
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84 [Libraries]
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85 Library_0=mainlib
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86 Library_1=
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87 Library_2=
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88 Library_3=
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89 Library_4=
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90 Library_5=
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91 Library_6=
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92 Library_7=
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93 Library_8=
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94 Library_9=
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95 Library_10=
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96 Library_11=
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97 Library_12=
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98 Library_13=
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99 Library_14=
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100 Library_15=
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101 Order_0=1 1
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102 Order_1=1 1
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103 Order_2=1 1
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104 Order_3=1 1
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105 Order_4=1 1
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106 Order_5=1 1
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107 Order_6=1 1
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108 Order_7=1 1
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109 Order_8=1 1
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110 Order_9=1 1
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111 [ICHI]
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112 On=1
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113 Isotope=1
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114 Stereo=0
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115 Derivative=1
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116 [Import]
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117 Dir=C:\NISTDEMO\MSSEARCH\
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118 Synonyms=1
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119 Filter=1
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120 Coeff=1 0
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121 [Structure Import]
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122 Dir=C:\NISTDEMO\MSSEARCH\
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123 Filter=1
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124 [Export]
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125 Dir=C:\NISTDEMO\MSSEARCH\
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126 Synonyms=1
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127 Filter=1
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128 Coeff=1 0
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129 [Search Options]
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130 Automatic=1
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131 [Library Search]
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132 SpecList Tab=1
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133 Placement_flags=2
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134 Placement_show=3
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135 ;Layout=1
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136 ;Hit Splitter Orientation=1
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137 ;List Tab=0
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138 ;Compare Tab=0
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139 ;Hit Tab=0
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140 ;Unknown Tab=0
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141 Placement_minx=-1
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142 Placement_miny=-1
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143 ;Placement_maxx=-4
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144 Placement_maxx=-8
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145 ;Placement_maxy=-23
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146 Placement_maxy=-30
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147 Placement_left=0
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148 Placement_top=1
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149 Placement_right=678
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150 Placement_bottom=397
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151 Splitter=0.314139
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152 List Splitter=0 0
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153 Unknown Splitter=0.493119
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154 Unknown Splitter Orientation=1
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155 ;Compare Splitter=0.3333 0.3333
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156 Compare Splitter=0 0
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157 Hit Splitter=0.493874
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158 SpecList Splitter=0.493119
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159 SpecList Splitter Orientation=1
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160 Hits Column=10 41 39 58 68 56 256 0 0 0 0
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161 ;SpecList Column=3 41 41 56
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162 ;SpecList Column=3 41 41 156
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163 SpecList Column=10 41 38 128 0 0 48 0 0 0 0
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164 Layout=1
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165 Hit Splitter Orientation=1
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166 List Tab=0
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167 Compare Tab=0
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168 Hit Tab=0
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169 Unknown Tab=0
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170 Replicates=0
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171 Exact Match=0
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172 [BAR-Summary]
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173 Bars=4
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174 ScreenCX=1600
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175 ScreenCY=900
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176 [REPORT]
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177 Ten Largest Peaks=1
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178 Compound Info=1
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179 Mass Intensity List=0
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180 Synonyms=1
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181 Plot=1
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182 Structure=1
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183 First Hits=1
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184 First Hits Number=3
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185 Unknown=0
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186 [Substructure Export]
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187 Filter=1
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188 Dir=
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189 [Substructure Import]
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190 Filter=1
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191 Dir=
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192 [Search AnyPeaks Options]
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193 Other=0
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194 Peaks=0
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195 Hitlist size=100
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196 Peak0=
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197 Peak1=
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198 Peak2=
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199 Peak3=
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200 Peak4=
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201 Peak5=
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202 Peak6=
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203 Peak7=
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204 Peak8=
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205 Peak9=
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206 Peak10=
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207 [Other Searches Options]
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208 CAS=
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209 MW=1
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210 ID=
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211 EPA=
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212 Formula=
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213 Seq Hitlist size=100
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214 [Constraints]
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215 Library ON=0
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216 Formula ON=0
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217 MW ON=0
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218 AnyPeaks ON=0
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219 Sequentiial ON=0
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220 Active MW=0
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221 MINMW=1
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222 MAXMW=2000
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223 Active Name=0
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224 Name Fragment=
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225 Elements Value=0
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226 Elements Present=0
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227 Mode Elements=0
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228 Num Elements=0
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229 Elements0=
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230 Elements1=
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231 Elements2=
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232 Elements3=
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233 Elements4=
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234 Elements5=
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235 Elements6=
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236 Elements7=
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237 Elements8=
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238 Elements9=
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239 Num Compare Elements=0
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240 Compare Elements0=
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241 Compare Elements1=
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242 Compare Elements2=
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243 Compare Elements3=
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244 Compare Elements4=
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245 Compare Elements5=
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246 Compare Elements6=
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247 Compare Elements7=
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248 Compare Elements8=
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249 Compare Elements9=
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250 Active Peaks=0
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251 Mode Peaks=1
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252 Num AnyPeaks=0
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253 Active OtherDB=0
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254 OtherDB=0
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255 Active Tags=0
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256 Tags=
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257 Active Peptide Sequence=0
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258 Peptide Sequence=
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259 Active Proton=0
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260 Proton Mode=0
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261 Proton Low=
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262 Proton Hi=
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263 Proton Exact=
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264 Active Charge=0
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265 Charge Mode=0
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266 Charge Low=
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267 Charge Hi=
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268 Charge Exact=
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269 Active Residue=0
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270 Residue Mode=0
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271 Residue Low=
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272 Residue Hi=
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273 Residue Exact=
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274 [Peptide Search Options]
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275 Cysteine Modification=0
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276 Comment Fields=
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277 Show Fields On Plot=1
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278 TF qry=0
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279 E Omssa=0
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280 TF lib=0
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281 RevImp=0
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282 Weight Omssa=0
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283 Weight Num Rep=0
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284 Weight Qtof=0
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285 Treshold=0
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286 [Library Hit]
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287 Font Name=MS Shell Dlg
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288 Font Pts=-8
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289 Font Width=0
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290 Font Esc=0
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291 Font Orientation=0
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292 Font Weight=400
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293 Font IUSC=0
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294 Font PCQP=654311424
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295 Color=0 255 16711680 16777215 16777215 0
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296 Order Number=1
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297 Structure Only=0
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298 Library=0
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299 Structure Size=50
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300 Match=1
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301 Probability=1
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302 Reverse Match=1
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303 Clear History=0
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304 [Library Spec List]
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305 Font Name=MS Shell Dlg
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306 Font Pts=-8
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307 Font Width=0
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308 Font Esc=0
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309 Font Orientation=0
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310 Font Weight=400
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311 Font IUSC=0
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312 Font PCQP=654311424
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313 Color=0 255 16711680 16777215 16777215 0
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314 Order Number=1
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315 Structure Only=0
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316 Library=0
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317 Structure Size=50
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318 Match=0
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319 Probability=0
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320 Reverse Match=0
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321 Clear History=0
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322 [Library Unknown Plot]
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323 Font Name=MS Shell Dlg
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324 Font Pts=-8
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325 Font Width=0
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326 Font Esc=0
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327 Font Orientation=0
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328 Font Weight=400
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329 Font IUSC=0
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330 Font PCQP=654311424
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331 Color=0 255 16711680 0 255 16777215
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332 Limits ON=0
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333 Wrap=0
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334 MW=0
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335 CAS=0
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336 Formula=0
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337 Threshold=0
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338 Structure=1
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339 Width=1
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340 Mass Label=1
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341 Pep Label=0
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342 [Library Hit Plot]
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343 Font Name=MS Shell Dlg
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344 Font Pts=-8
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345 Font Width=0
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346 Font Esc=0
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347 Font Orientation=0
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348 Font Weight=400
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349 Font IUSC=0
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350 Font PCQP=654311424
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351 Color=0 255 16711680 0 255 16777215
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352 Limits ON=0
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353 Wrap=0
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354 MW=1
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355 CAS=0
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356 Formula=1
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357 Threshold=0
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358 Structure=1
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359 Width=1
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360 Mass Label=1
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361 Pep Label=0
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362 [Library SpecList Plot]
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363 Font Name=MS Shell Dlg
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364 Font Pts=-8
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365 Font Width=0
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366 Font Esc=0
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367 Font Orientation=0
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368 Font Weight=400
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369 Font IUSC=0
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370 Font PCQP=654311424
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371 Color=0 255 16711680 0 255 16777215
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372 Limits ON=0
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373 Wrap=0
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374 MW=0
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375 CAS=0
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376 Formula=0
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377 Threshold=0
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378 Structure=1
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379 Width=1
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380 Mass Label=1
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381 Pep Label=0
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382 [Library Unknown Text]
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383 Font Name=MS Shell Dlg
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384 Font Pts=-8
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385 Font Width=0
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386 Font Esc=0
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387 Font Orientation=0
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388 Font Weight=400
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389 Font IUSC=0
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390 Font PCQP=654311424
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391 Color=16711680 0 255 8421376 16777215
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392 Ten Peaks=1
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393 Compound=1
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394 Intensity=0
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395 Synonyms=1
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396 Rows=0
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397 Noise=0
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398 Wrap Synonyms=0
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399 RI=1
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400 RI All=1
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401 RI Num=2
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402 [Library Hit Text]
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403 Font Name=MS Shell Dlg
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404 Font Pts=-8
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405 Font Width=0
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406 Font Esc=0
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407 Font Orientation=0
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408 Font Weight=400
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409 Font IUSC=0
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410 Font PCQP=654311424
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411 Color=16711680 0 255 8421376 16777215
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412 Ten Peaks=1
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413 Compound=1
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414 Intensity=1
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415 Synonyms=1
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416 Rows=0
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417 Noise=0
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418 Wrap Synonyms=0
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419 RI=1
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420 RI All=1
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421 RI Num=2
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422 [Library SpecList Text]
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423 Font Name=MS Shell Dlg
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424 Font Pts=-8
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425 Font Width=0
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426 Font Esc=0
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427 Font Orientation=0
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428 Font Weight=400
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429 Font IUSC=0
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430 Font PCQP=654311424
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431 Color=16711680 0 255 8421376 16777215
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432 Ten Peaks=1
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433 Compound=1
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434 Intensity=0
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435 Synonyms=1
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436 Rows=0
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437 Noise=0
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438 Wrap Synonyms=0
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439 RI=1
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440 RI All=1
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441 RI Num=2
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442 [Library Compare]
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443 Font Name=MS Shell Dlg
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444 Font Pts=-8
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445 Font Width=0
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446 Font Esc=0
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447 Font Orientation=0
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448 Font Weight=400
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449 Font IUSC=0
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450 Font PCQP=654311424
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451 Color=0 255 16711680 32768 16777215
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452 Limit ON=0
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453 Threshold=0
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454 Show=1
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455 Show Structure=0
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456 Independent Zoom=0
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457 Width=1
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458 [Library Histogram]
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459 Font Name=MS Shell Dlg
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460 Font Pts=-8
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461 Font Width=0
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462 Font Esc=0
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463 Font Orientation=0
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464 Font Weight=400
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465 Font IUSC=0
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466 Font PCQP=654311424
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467 Color=0 16711680 255 16777215
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468 Discret=25
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469 Axis=1
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470 Automatic=1
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471 Min=0
|
|
|
472 Max=1000
|
|
|
473 [Library Display]
|
|
|
474 Neutral Loss=0
|
|
|
475 Scale=0
|
|
|
476 Min mz=0
|
|
|
477 Max mz=1000
|
|
|
478 Default Search Anchor=1
|
|
|
479 Search Anchor=0
|
|
|
480 Default Hit Anchor=1
|
|
|
481 Hit Anchor=0
|
|
|
482 Max Loss=70
|
|
|
483 mz=10
|
|
|
484 [Incremental Search]
|
|
|
485 Placement_flags=0
|
|
|
486 Placement_show=1
|
|
|
487 Placement_minx=-1
|
|
|
488 Placement_miny=-1
|
|
|
489 Placement_maxx=-8
|
|
|
490 Placement_maxy=-30
|
|
|
491 Placement_left=50
|
|
|
492 Placement_top=50
|
|
|
493 Placement_right=1269
|
|
|
494 Placement_bottom=449
|
|
|
495 Key=10METHOXYDESERPID
|
|
|
496 Splitter=0.333054
|
|
|
497 Layout=1
|
|
|
498 Plot Splitter=0.5
|
|
|
499 Plot Splitter Orientation=0
|
|
|
500 List Tab=0
|
|
|
501 Spectrum Tab=0
|
|
|
502 Alpha=0
|
|
|
503 [Incremental View]
|
|
|
504 Font Name=MS Shell Dlg
|
|
|
505 Font Pts=-8
|
|
|
506 Font Width=0
|
|
|
507 Font Esc=0
|
|
|
508 Font Orientation=0
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|
509 Font Weight=400
|
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|
510 Font IUSC=0
|
|
|
511 Font PCQP=654311424
|
|
|
512 Color=0 255 16711680 16777215 16777215 0
|
|
|
513 Auto Display=1
|
|
|
514 Structure Only=50
|
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|
515 [Incremental Plot]
|
|
|
516 Font Name=MS Shell Dlg
|
|
|
517 Font Pts=-8
|
|
|
518 Font Width=0
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|
519 Font Esc=0
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|
520 Font Orientation=0
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|
|
521 Font Weight=400
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|
522 Font IUSC=0
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|
523 Font PCQP=654311424
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|
|
524 Color=0 255 16711680 0 255 16777215
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|
|
525 Limits ON=0
|
|
|
526 Wrap=0
|
|
|
527 MW=0
|
|
|
528 CAS=0
|
|
|
529 Formula=0
|
|
|
530 Threshold=0
|
|
|
531 Structure=1
|
|
|
532 Width=1
|
|
|
533 Mass Label=1
|
|
|
534 Pep Label=0
|
|
|
535 [Incremental Text]
|
|
|
536 Font Name=MS Shell Dlg
|
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|
537 Font Pts=-8
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|
538 Font Width=0
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|
539 Font Esc=0
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540 Font Orientation=0
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541 Font Weight=400
|
|
|
542 Font IUSC=0
|
|
|
543 Font PCQP=654311424
|
|
|
544 Color=16711680 0 255 8421376 16777215
|
|
|
545 Ten Peaks=1
|
|
|
546 Compound=1
|
|
|
547 Intensity=0
|
|
|
548 Synonyms=1
|
|
|
549 Rows=0
|
|
|
550 Noise=0
|
|
|
551 Wrap Synonyms=0
|
|
|
552 RI=1
|
|
|
553 RI All=1
|
|
|
554 RI Num=2
|
|
|
555 [Other Search]
|
|
|
556 Placement_flags=0
|
|
|
557 Placement_show=1
|
|
|
558 Placement_minx=-1
|
|
|
559 Placement_miny=-1
|
|
|
560 Placement_maxx=-8
|
|
|
561 Placement_maxy=-30
|
|
|
562 Placement_left=25
|
|
|
563 Placement_top=25
|
|
|
564 Placement_right=1244
|
|
|
565 Placement_bottom=424
|
|
|
566 Splitter=0.332215
|
|
|
567 Layout=1
|
|
|
568 Plot Splitter=0.5
|
|
|
569 Plot Splitter Orientation=0
|
|
|
570 List Tab=0
|
|
|
571 Spectrum Tab=0
|
|
|
572 Replicates=0
|
|
|
573 Search Mode=2
|
|
|
574 Column=10 39 37 0 0 0 48 0 0 0 0
|
|
|
575 [Other Hit]
|
|
|
576 Font Name=MS Shell Dlg
|
|
|
577 Font Pts=-8
|
|
|
578 Font Width=0
|
|
|
579 Font Esc=0
|
|
|
580 Font Orientation=0
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|
|
581 Font Weight=400
|
|
|
582 Font IUSC=0
|
|
|
583 Font PCQP=654311424
|
|
|
584 Color=0 255 16711680 16777215 16777215 0
|
|
|
585 Order Number=1
|
|
|
586 Structure Only=0
|
|
|
587 Library=0
|
|
|
588 Structure Size=50
|
|
|
589 Match=0
|
|
|
590 Probability=0
|
|
|
591 Reverse Match=0
|
|
|
592 Clear History=0
|
|
|
593 [Other Plot]
|
|
|
594 Font Name=MS Shell Dlg
|
|
|
595 Font Pts=-8
|
|
|
596 Font Width=0
|
|
|
597 Font Esc=0
|
|
|
598 Font Orientation=0
|
|
|
599 Font Weight=400
|
|
|
600 Font IUSC=0
|
|
|
601 Font PCQP=654311424
|
|
|
602 Color=0 255 16711680 0 255 16777215
|
|
|
603 Limits ON=0
|
|
|
604 Wrap=0
|
|
|
605 MW=0
|
|
|
606 CAS=0
|
|
|
607 Formula=0
|
|
|
608 Threshold=0
|
|
|
609 Structure=1
|
|
|
610 Width=1
|
|
|
611 Mass Label=1
|
|
|
612 Pep Label=0
|
|
|
613 [Other Text]
|
|
|
614 Font Name=MS Shell Dlg
|
|
|
615 Font Pts=-8
|
|
|
616 Font Width=0
|
|
|
617 Font Esc=0
|
|
|
618 Font Orientation=0
|
|
|
619 Font Weight=400
|
|
|
620 Font IUSC=0
|
|
|
621 Font PCQP=654311424
|
|
|
622 Color=16711680 0 255 8421376 16777215
|
|
|
623 Ten Peaks=1
|
|
|
624 Compound=1
|
|
|
625 Intensity=0
|
|
|
626 Synonyms=1
|
|
|
627 Rows=0
|
|
|
628 Noise=0
|
|
|
629 Wrap Synonyms=0
|
|
|
630 RI=1
|
|
|
631 RI All=1
|
|
|
632 RI Num=2
|
|
|
633 [Compare]
|
|
|
634 Placement_flags=0
|
|
|
635 Placement_show=1
|
|
|
636 Placement_minx=-1
|
|
|
637 Placement_miny=-1
|
|
|
638 Placement_maxx=-8
|
|
|
639 Placement_maxy=-30
|
|
|
640 Placement_left=75
|
|
|
641 Placement_top=75
|
|
|
642 Placement_right=1294
|
|
|
643 Placement_bottom=474
|
|
|
644 Splitter=0.244898 0.244898
|
|
|
645 Tab=0
|
|
|
646 [Compare Plot]
|
|
|
647 Font Name=MS Shell Dlg
|
|
|
648 Font Pts=-8
|
|
|
649 Font Width=0
|
|
|
650 Font Esc=0
|
|
|
651 Font Orientation=0
|
|
|
652 Font Weight=400
|
|
|
653 Font IUSC=0
|
|
|
654 Font PCQP=654311424
|
|
|
655 Color=0 255 16711680 0 255 16777215
|
|
|
656 Limits ON=0
|
|
|
657 Wrap=0
|
|
|
658 MW=0
|
|
|
659 CAS=0
|
|
|
660 Formula=0
|
|
|
661 Threshold=0
|
|
|
662 Structure=1
|
|
|
663 Width=1
|
|
|
664 Mass Label=1
|
|
|
665 Pep Label=0
|
|
|
666 [Compare Result]
|
|
|
667 Font Name=MS Shell Dlg
|
|
|
668 Font Pts=-8
|
|
|
669 Font Width=0
|
|
|
670 Font Esc=0
|
|
|
671 Font Orientation=0
|
|
|
672 Font Weight=400
|
|
|
673 Font IUSC=0
|
|
|
674 Font PCQP=654311424
|
|
|
675 Color=0 255 16711680 32768 16777215
|
|
|
676 Limit ON=0
|
|
|
677 Threshold=0
|
|
|
678 Show=1
|
|
|
679 Show Structure=0
|
|
|
680 Independent Zoom=0
|
|
|
681 Width=1
|
|
|
682 [Compare List]
|
|
|
683 Font Name=MS Shell Dlg
|
|
|
684 Font Pts=-8
|
|
|
685 Font Width=0
|
|
|
686 Font Esc=0
|
|
|
687 Font Orientation=0
|
|
|
688 Font Weight=400
|
|
|
689 Font IUSC=0
|
|
|
690 Font PCQP=654311424
|
|
|
691 Color=32768 0 255 16711680 16777215 0 255
|
|
|
692 Names=1
|
|
|
693 No Structure=0
|
|
|
694 Limits ON=0
|
|
|
695 Threshold=0
|
|
|
696 Spectra on Page=3
|
|
|
697 Overwrite=1
|
|
|
698 Insert=1
|
|
|
699 Hits=3
|
|
|
700 Wrap=0
|
|
|
701 MW=0
|
|
|
702 CAS=0
|
|
|
703 Formula=0
|
|
|
704 Width=1
|
|
|
705 Mass Label=1
|
|
|
706 Pep Label=0
|
|
|
707 [Compare Display]
|
|
|
708 Neutral Loss=0
|
|
|
709 Scale=0
|
|
|
710 Min mz=0
|
|
|
711 Max mz=1000
|
|
|
712 Default Search Anchor=1
|
|
|
713 Search Anchor=0
|
|
|
714 Default Hit Anchor=1
|
|
|
715 Hit Anchor=0
|
|
|
716 Max Loss=70
|
|
|
717 mz=10
|
|
|
718 [SpecList]
|
|
|
719 Placement_flags=0
|
|
|
720 Placement_show=1
|
|
|
721 Placement_minx=-1
|
|
|
722 Placement_miny=-1
|
|
|
723 Placement_maxx=-8
|
|
|
724 Placement_maxy=-30
|
|
|
725 Placement_left=100
|
|
|
726 Placement_top=100
|
|
|
727 Placement_right=1319
|
|
|
728 Placement_bottom=499
|
|
|
729 Splitter=0.333054
|
|
|
730 Layout=1
|
|
|
731 Plot Splitter=0.5
|
|
|
732 Plot Splitter Orientation=0
|
|
|
733 List Tab=0
|
|
|
734 Spectrum Tab=0
|
|
|
735 Column=10 39 39 0 0 0 48 0 0 0 0
|
|
|
736 [SpecList Hit]
|
|
|
737 Font Name=MS Shell Dlg
|
|
|
738 Font Pts=-8
|
|
|
739 Font Width=0
|
|
|
740 Font Esc=0
|
|
|
741 Font Orientation=0
|
|
|
742 Font Weight=400
|
|
|
743 Font IUSC=0
|
|
|
744 Font PCQP=654311424
|
|
|
745 Color=0 255 16711680 16777215 16777215 0
|
|
|
746 Order Number=1
|
|
|
747 Structure Only=0
|
|
|
748 Library=0
|
|
|
749 Structure Size=50
|
|
|
750 Match=0
|
|
|
751 Probability=0
|
|
|
752 Reverse Match=0
|
|
|
753 Clear History=0
|
|
|
754 [SpecList Plot]
|
|
|
755 Font Name=MS Shell Dlg
|
|
|
756 Font Pts=-8
|
|
|
757 Font Width=0
|
|
|
758 Font Esc=0
|
|
|
759 Font Orientation=0
|
|
|
760 Font Weight=400
|
|
|
761 Font IUSC=0
|
|
|
762 Font PCQP=654311424
|
|
|
763 Color=0 255 16711680 0 255 16777215
|
|
|
764 Limits ON=0
|
|
|
765 Wrap=0
|
|
|
766 MW=0
|
|
|
767 CAS=0
|
|
|
768 Formula=0
|
|
|
769 Threshold=0
|
|
|
770 Structure=1
|
|
|
771 Width=1
|
|
|
772 Mass Label=1
|
|
|
773 Pep Label=0
|
|
|
774 [SpecList Text]
|
|
|
775 Font Name=MS Shell Dlg
|
|
|
776 Font Pts=-8
|
|
|
777 Font Width=0
|
|
|
778 Font Esc=0
|
|
|
779 Font Orientation=0
|
|
|
780 Font Weight=400
|
|
|
781 Font IUSC=0
|
|
|
782 Font PCQP=654311424
|
|
|
783 Color=16711680 0 255 8421376 16777215
|
|
|
784 Ten Peaks=1
|
|
|
785 Compound=1
|
|
|
786 Intensity=0
|
|
|
787 Synonyms=1
|
|
|
788 Rows=0
|
|
|
789 Noise=0
|
|
|
790 Wrap Synonyms=0
|
|
|
791 RI=1
|
|
|
792 RI All=1
|
|
|
793 RI Num=2
|
|
|
794 [BAR-Bar0]
|
|
|
795 BarID=59419
|
|
|
796 Bars=5
|
|
|
797 Bar#0=0
|
|
|
798 Bar#1=59647
|
|
|
799 Bar#2=0
|
|
|
800 Bar#3=59392
|
|
|
801 Bar#4=0
|
|
|
802 [BAR-Bar1]
|
|
|
803 BarID=59393
|
|
|
804 MRUWidth=0
|
|
|
805 [BAR-Bar2]
|
|
|
806 BarID=59647
|
|
|
807 MRUWidth=288
|
|
|
808 Docking=1
|
|
|
809 MRUDockID=0
|
|
|
810 MRUDockLeftPos=-1
|
|
|
811 MRUDockTopPos=-1
|
|
|
812 MRUDockRightPos=1599
|
|
|
813 MRUDockBottomPos=28
|
|
|
814 MRUFloatStyle=8196
|
|
|
815 MRUFloatXPos=-2147483648
|
|
|
816 MRUFloatYPos=0
|
|
|
817 [BAR-Bar3]
|
|
|
818 BarID=59392
|
|
|
819 YPos=28
|
|
|
820 MRUWidth=276
|
|
|
821 Docking=1
|
|
|
822 MRUDockID=0
|
|
|
823 MRUDockLeftPos=-1
|
|
|
824 MRUDockTopPos=28
|
|
|
825 MRUDockRightPos=294
|
|
|
826 MRUDockBottomPos=61
|
|
|
827 MRUFloatStyle=8196
|
|
|
828 MRUFloatXPos=-2147483648
|
|
|
829 MRUFloatYPos=0</configfile>
|
|
|
830
|
|
|
831 </configfiles>
|
|
|
832
|
|
|
833 <outputs>
|
|
|
834 <data name="outputFile" format="tabular" label="${tool.name} on ${on_string} - NIST library matches (TSV)"/>
|
|
3
|
835 <data name="outputFileFinal" format="tabular" label="${tool.name} on ${on_string} - NIST library matches (TSV)"/>
|
|
0
|
836 <data name="outputLog" format="txt" label="${tool.name} on ${on_string} - LOG" hidden="True"/>
|
|
|
837 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - NIST matches report (HTML)"/>
|
|
|
838 </outputs>
|
|
|
839 <tests>
|
|
|
840 <test>
|
|
|
841 </test>
|
|
|
842 </tests>
|
|
|
843 <help>
|
|
|
844
|
|
|
845 .. class:: infomark
|
|
|
846
|
|
|
847 Runs the process also used by NIST mssearch (see screenshot), executing it in batch mode and returning the produced results
|
|
|
848 file with the library matches found for each input spectrum found in the given spectra file.
|
|
|
849
|
|
|
850 .. image:: $PATH_TO_IMAGES/NIST_mssearch_screenshot.png
|
|
|
851
|
|
|
852
|
|
|
853 .. class:: infomark
|
|
|
854
|
|
|
855 This tool requires a valid NIST folder and respective (licensed) libraries to be present on your server.
|
|
|
856 Check http://chemdata.nist.gov/mass-spc/ms-search/ for more information.
|
|
|
857
|
|
|
858 *References*
|
|
|
859
|
|
|
860 NIST Mass Spectral Search Program (Version 2.2)
|
|
|
861
|
|
|
862 http://chemdata.nist.gov/mass-spc/ms-search/docs/Ver20Man_11.pdf
|
|
|
863
|
|
|
864
|
|
|
865 For additional information, see Stein, S.E. “Optimization and Testing of Mass Spectral Library
|
|
|
866 Search Algorithms for Compound Identification” J. Am. Soc. Mass Spectrom. 1994, 5, 859–865.
|
|
|
867
|
|
|
868 </help>
|
|
|
869 </tool> |
