annotate nist_wrapper.xml @ 1:964ec10d568c

new NIST wrapper demo tools
author pieter.lukasse@wur.nl
date Thu, 22 Jan 2015 16:15:30 +0100
parents cce6989ed423
children f6da901ffff8
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1 <tool id="nist_wrapper" name="NIST MSSEARCH" version="0.0.1">
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2 <!--
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3 This part is a WORKAROUND for the wine X11 dependency, allowing it to run headless :
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4 -> install Xvfb and enable it on a port, say 995:
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5 -> make sure this gets executed: export DISPLAY=:995;
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6 -->
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7 <description> Runs NIST's msseach program to match spectra against metabolite libraries</description>
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8 <command interpreter="export DISPLAY=:0; python">
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9 nist_wrapper.py
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10 "~/.wine/drive_c/NIST"
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11 $nistIniFile
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12 $spectraFile
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13 $outputFile
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14 </command>
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15 <inputs>
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16 <param name="spectraFile" type="data" format="msp" label="Spectra file (.MSP)" help="E.g. file produced by MsClust"/>
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17
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18 <param name="hitsToReport" type="integer" size="10" value="3" label="Number of matches to report per spetrum"
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19 help="Top X matches for each spectrum will be written to output file." />
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20
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21 </inputs>
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22 <configfiles>
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23
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24 <configfile name="nistIniFile">[MAIN]
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25 Version=2.0
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26 Library Directory=C:\NISTDEMO\MSSEARCH\
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27 Program=NIST MS
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28 Active Frame=0
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29 Placement_flags=2
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30 Placement_show=3
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31 Placement_minx=-32000
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32 Placement_miny=-32000
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33 Placement_maxx=-1
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34 Placement_maxy=-1
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35 Placement_left=0
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36 Placement_top=84
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37 Placement_right=1440
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38 Placement_bottom=827
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39 Wrong Libraries=
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40 Active Show=3
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41 Display Warning=1
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42 Display Info=0
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43 [Search Options]
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44 Automatic=1
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45 Type=1
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46 As MW=1
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47 MW=1
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48 Reverse=0
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49 Penalize=0
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50 Search with MW=1
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51 Preasearch=0
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52 Apply Limits=0
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53 Min Mass Type=0
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54 Min Mass=1
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55 Max Mass ON=0
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56 Max Mass=2000
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57 Min Abund ON=0
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58 Min Abund=1
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59 Printing=0
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60 Return Focus=0
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61 Hits to Print=${hitsToReport}
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62 Print Spectra=1
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63 Print Structure=1
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64 Apply MaxLength=0
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65 MaxLength=2000
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66 Sort Mode=0
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67 Match Clusters=1
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68 Match Rings=1
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69 Weighting=0
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70 Use Specified Parent=0
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71 Ignore Precursor=0
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72 Parent Mass=0
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73 Precursor Tolerance=1.6
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74 Ions Tolerance=0.8
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75 [Libraries]
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76 Library_0=mainlib
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77 Library_1=
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78 Library_2=
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79 Library_3=
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80 Library_4=
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81 Library_5=
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82 Library_6=
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83 Library_7=
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84 Library_8=
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85 Library_9=
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86 Library_10=
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87 Library_11=
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88 Library_12=
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89 Library_13=
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90 Library_14=
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91 Library_15=
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92 Order_0=1 1
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93 Order_1=1 1
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94 Order_2=1 1
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95 Order_3=1 1
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96 Order_4=1 1
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97 Order_5=1 1
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98 Order_6=1 1
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99 Order_7=1 1
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100 Order_8=1 1
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101 Order_9=1 1
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102 [ICHI]
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103 On=1
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104 Isotope=1
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105 Stereo=0
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106 Derivative=1
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107 [Import]
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108 Dir=C:\NISTDEMO\MSSEARCH\
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109 Synonyms=1
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110 Filter=1
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111 Coeff=1 0
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112 [Structure Import]
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113 Dir=C:\NISTDEMO\MSSEARCH\
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114 Filter=1
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115 [Export]
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116 Dir=C:\NISTDEMO\MSSEARCH\
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117 Synonyms=1
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118 Filter=1
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119 Coeff=1 0
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120 [Search Options]
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121 Automatic=1
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122 [Library Search]
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123 SpecList Tab=1
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124 Placement_flags=2
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125 Placement_show=3
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126 ;Layout=1
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127 ;Hit Splitter Orientation=1
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128 ;List Tab=0
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129 ;Compare Tab=0
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130 ;Hit Tab=0
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131 ;Unknown Tab=0
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132 Placement_minx=-1
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133 Placement_miny=-1
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134 ;Placement_maxx=-4
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135 Placement_maxx=-8
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136 ;Placement_maxy=-23
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137 Placement_maxy=-30
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138 Placement_left=0
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139 Placement_top=1
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140 Placement_right=678
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141 Placement_bottom=397
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142 Splitter=0.314139
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143 List Splitter=0 0
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144 Unknown Splitter=0.493119
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145 Unknown Splitter Orientation=1
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146 ;Compare Splitter=0.3333 0.3333
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147 Compare Splitter=0 0
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148 Hit Splitter=0.493874
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149 SpecList Splitter=0.493119
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150 SpecList Splitter Orientation=1
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151 Hits Column=10 41 39 58 68 56 256 0 0 0 0
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152 ;SpecList Column=3 41 41 56
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153 ;SpecList Column=3 41 41 156
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154 SpecList Column=10 41 38 128 0 0 48 0 0 0 0
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155 Layout=1
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156 Hit Splitter Orientation=1
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157 List Tab=0
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158 Compare Tab=0
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159 Hit Tab=0
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160 Unknown Tab=0
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161 Replicates=0
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162 Exact Match=0
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163 [BAR-Summary]
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164 Bars=4
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165 ScreenCX=1600
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166 ScreenCY=900
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167 [REPORT]
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168 Ten Largest Peaks=1
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169 Compound Info=1
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170 Mass Intensity List=0
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171 Synonyms=1
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172 Plot=1
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173 Structure=1
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174 First Hits=1
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175 First Hits Number=3
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176 Unknown=0
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177 [Substructure Export]
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178 Filter=1
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735 Font PCQP=654311424
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736 Color=0 255 16711680 16777215 16777215 0
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737 Order Number=1
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738 Structure Only=0
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739 Library=0
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740 Structure Size=50
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741 Match=0
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742 Probability=0
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743 Reverse Match=0
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744 Clear History=0
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746 Font Name=MS Shell Dlg
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747 Font Pts=-8
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748 Font Width=0
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749 Font Esc=0
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750 Font Orientation=0
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751 Font Weight=400
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752 Font IUSC=0
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753 Font PCQP=654311424
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754 Color=0 255 16711680 0 255 16777215
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755 Limits ON=0
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756 Wrap=0
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757 MW=0
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758 CAS=0
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759 Formula=0
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760 Threshold=0
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761 Structure=1
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762 Width=1
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763 Mass Label=1
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764 Pep Label=0
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765 [SpecList Text]
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766 Font Name=MS Shell Dlg
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767 Font Pts=-8
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768 Font Width=0
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769 Font Esc=0
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772 Font IUSC=0
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773 Font PCQP=654311424
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774 Color=16711680 0 255 8421376 16777215
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775 Ten Peaks=1
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776 Compound=1
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777 Intensity=0
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778 Synonyms=1
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779 Rows=0
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780 Noise=0
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781 Wrap Synonyms=0
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782 RI=1
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783 RI All=1
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784 RI Num=2
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785 [BAR-Bar0]
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786 BarID=59419
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787 Bars=5
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788 Bar#0=0
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789 Bar#1=59647
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790 Bar#2=0
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791 Bar#3=59392
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792 Bar#4=0
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793 [BAR-Bar1]
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794 BarID=59393
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795 MRUWidth=0
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796 [BAR-Bar2]
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797 BarID=59647
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798 MRUWidth=288
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799 Docking=1
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800 MRUDockID=0
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801 MRUDockLeftPos=-1
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802 MRUDockTopPos=-1
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803 MRUDockRightPos=1599
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804 MRUDockBottomPos=28
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805 MRUFloatStyle=8196
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806 MRUFloatXPos=-2147483648
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807 MRUFloatYPos=0
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808 [BAR-Bar3]
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809 BarID=59392
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810 YPos=28
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811 MRUWidth=276
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812 Docking=1
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813 MRUDockID=0
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814 MRUDockLeftPos=-1
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815 MRUDockTopPos=28
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816 MRUDockRightPos=294
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817 MRUDockBottomPos=61
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818 MRUFloatStyle=8196
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819 MRUFloatXPos=-2147483648
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820 MRUFloatYPos=0</configfile>
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821
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822 </configfiles>
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823
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824 <outputs>
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825 <data name="outputFile" format="tabular" label="${tool.name} on ${on_string} - NIST library matches (TSV)"/>
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826 <data name="outputLog" format="txt" label="${tool.name} on ${on_string} - LOG" hidden="True"/>
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827 <data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - NIST matches report (HTML)"/>
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828 </outputs>
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829 <tests>
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830 <test>
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831 </test>
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832 </tests>
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833 <help>
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834
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835 .. class:: infomark
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836
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837 Runs the process also used by NIST mssearch (see screenshot), executing it in batch mode and returning the produced results
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838 file with the library matches found for each input spectrum found in the given spectra file.
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839
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840 .. image:: $PATH_TO_IMAGES/NIST_mssearch_screenshot.png
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841
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842
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843 .. class:: infomark
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844
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845 This tool requires a valid NIST folder and respective (licensed) libraries to be present on your server.
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846 Check http://chemdata.nist.gov/mass-spc/ms-search/ for more information.
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847
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diff changeset
848 *References*
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849
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850 NIST Mass Spectral Search Program (Version 2.2)
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851
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852 http://chemdata.nist.gov/mass-spc/ms-search/docs/Ver20Man_11.pdf
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853
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854
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855 For additional information, see Stein, S.E. “Optimization and Testing of Mass Spectral Library
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856 Search Algorithms for Compound Identification” J. Am. Soc. Mass Spectrom. 1994, 5, 859–865.
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857
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858 </help>
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859 </tool>