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