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annotate spectral_matching.xml @ 25:b6434344ff95 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 04023134d8f28e85927ca293373c506484149ead-dirty
author tomnl
date Mon, 04 Jun 2018 06:45:23 -0400
parents c6d0d9ae8f0b
children efebff661749
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1 <tool id="spectral_matching" name="spectral_matching" version="0.1.1">
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2 <description>
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3 Perform spectral matching to spectral libraries using dot product cosine on a MS/MS dataset
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4 </description>
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5
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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10 <expand macro="requirements">
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11 <requirement type="package" >bioconductor-mspuritydata</requirement>
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12 </expand>
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5
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0
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15 <stdio>
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16 <exit_code range="1:" />
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17 </stdio>
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18 <command interpreter="Rscript"><![CDATA[
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19 spectral_matching.R
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20 --out_dir=.
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21 --target_db_pth=$target_db
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23 #if $custom_sqlite.custom_sqlite_select=="yes"
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24 --library_db_pth=$library_db
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25 #end if
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27
0
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28 --ra_thres_l=$advanced.ra_thres_l
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29 --ra_thres_t=$advanced.ra_thres_t
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30 --cores=\${GALAXY_SLOTS:-4}
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31 --pol=$pol
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32 --score_thres=$score_thres
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33 --ppm_tol_prod=$ppm_tol_prod
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34 --ppm_tol_prec=$ppm_tol_prec
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35 --instrument_types=$instrument_types
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36 --library_sources=$library_sources
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37 #if $advanced.topncond.topnbool:
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38 --topn=$topn
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39 #end if
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40 #if $advanced.scan_ids:
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41 --scan_ids='
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42 #for $i, $j in enumerate($advanced.scan_ids)
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43 $j.scan_ids,
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44 #end for
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45 '
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46 #end if
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47 #if $create_new_database:
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48 --create_new_database
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49 #end if
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51
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52
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53 ]]></command>
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54 <inputs>
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55
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56 <param type="data" name="target_db" label="SQLite DB of target spectra" format="sqlite"
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57 help="SQLite DB of target spectra. (e.g. generated from frag4feature tool)"/>
14
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58
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59 <conditional name="custom_sqlite">
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60 <param name="custom_sqlite_select" type="select" label="Use custom library SQLite Database?">
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61 <option value="no" >no</option>
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62 <option value="yes" >yes</option>
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63 </param>
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64 <when value="no">
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65 </when>
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66 <when value="yes">
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67 <param type="data" name="library_db" label="SQLite DB of library spectra" format="sqlite"
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68 help="SQLite database of library (reference) spectra, if left blank will use the default
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69 library from msPurityData
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70 https://www.dropbox.com/s/csxj6pairsgd8fe/library_spectra.db?dl=1
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71 A more official location can be found here: https://bioconductor.org/packages/release/data/experiment/src/contrib/msPurityData_1.6.0.tar.gz
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72 "/>
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73 </when>
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74 </conditional>
0
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75
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76
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77 <param name="pol" type="select" label="polarity" >
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78 <option value="positive" selected="true">Positive</option>
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79 <option value="negative" >negative</option>
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80 </param>
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81
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82 <param name="ppm_tol_prod" type="float" value="10"
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83 help="Parts per million tolerance to match product mz values"/>
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84
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85 <param name="ppm_tol_prec" type="float" value="5"
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86 help="Parts per million tolerance to match precursor mz values"/>
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87
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88 <param name="score_thres" type="float" min="0" max="1" value="0.6"
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89 help="Dot product cosine score threshold"/>
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90
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91 <param name="instrument_types" type="select" multiple="true" >
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92 <option value="APCI-ITFT">APCI-ITFT</option>
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93 <option value="CE-ESI-TOF" selected="true">CE-ESI-TOF</option>
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94 <option value="CI-B">CI-B</option>
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95 <option value="EI-B">EI-B</option>
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96 <option value="EI-EBEB">EI-EBEB</option>
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97 <option value="ESI-ITFT" selected="true">ESI-ITFT</option>
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98 <option value="ESI-ITTOF" selected="true">ESI-ITTOF</option>
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99 <option value="ESI-QTOF" selected="true">ESI-QTOF</option>
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100 <option value="FAB-B">FAB-B</option>
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101 <option value="FAB-BE-MS">FAB-BE-MS</option>
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102 <option value="FAB-EB">FAB-EB</option>
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103 <option value="FAB-EBEB">FAB-EBEB</option>
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104 <option value="FI-B">FI-B</option>
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105 <option value="GC-EI-Q">GC-EI-Q</option>
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106 <option value="GC-EI-QQ">GC-EI-QQ</option>
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107 <option value="GC-EI-TOF">GC-EI-TOF</option>
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108 <option value="LC-APCI-QTOF">LC-APCI-QTOF</option>
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109 <option value="LC-APPI-QQ">LC-APPI-QQ</option>
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110 <option value="LC-ESI-IT" selected="true">LC-ESI-IT</option>
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111 <option value="LC-ESI-ITFT" selected="true">LC-ESI-ITFT</option>
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112 <option value="LC-ESI-ITTOF" selected="true">LC-ESI-ITTOF</option>
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113 <option value="LC-ESI-Q">LC-ESI-Q</option>
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114 <option value="LC-ESI-QFT" selected="true" >LC-ESI-QFT</option>
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115 <option value="LC-ESI-QIT" selected="true">LC-ESI-QIT</option>
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116 <option value="LC-ESI-QQ" selected="true">LC-ESI-QQ</option>
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117 <option value="LC-ESI-QTOF" selected="true">LC-ESI-QTOF</option>
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118 <option value="LC-ESI-TOF" selected="true">LC-ESI-TOF</option>
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119 <option value="MALDI-QIT">MALDI-QIT</option>
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120 <option value="MALDI-TOF">MALDI-TOF</option>
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121 <option value="ALDI-TOFTOF">ALDI-TOFTOF</option>
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122 </param>
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123
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124 <param name="library_sources" type="select" multiple="true" >
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125 <option value="lipidblast">LipidBlast</option>
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126 <option value="massbank" selected="true">MassBank</option>
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127 <option value="GNPS">GNPS</option>
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128 </param>
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129 <param name="create_new_database" type="boolean" checked="true" label="Create a new database for the results?"
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130 help="A copy will be made of the input SQLite target database and the results will be added to this copy.
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131 When False, the input SQLite database will be updated with the matching results. Use False
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132 if you want to reduce storage space being used."/>
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133
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134 <section name="advanced" title="advanced" expanded="False">
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135 <conditional name="topncond">
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136 <param name="topnbool" type="boolean" label="Only use the top n spectral matching hits?"/>
efb634ef71fd planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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137 <when value="false">
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138 </when>
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139 <when value="true">
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140 <param name="topn" type="integer" value="10" help="Only use top n matches"/>
efb634ef71fd planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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141 </when>
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142 </conditional>
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143
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144 <param name="ra_thres_l" type="float" value="0"
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145 help="Relative abundance threshold for library spectra"/>
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146
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147 <param name="ra_thres_t" type="float" value="2"
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148 help="Relative abundance threshold for target spectra (e.g. spectral data from users MS files)"/>
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149
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150 <repeat name="scan_ids" title="Specific scan ids">
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151 <param name="scan_ids" type="integer" value=""/>
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152 </repeat>
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153
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154
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155 </section>
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156
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157 </inputs>
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158 <outputs>
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159
efb634ef71fd planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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160
efb634ef71fd planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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161
efb634ef71fd planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c
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162 <data name="sqlite_results" format="sqlite" label="${tool.name} on ${on_string}: SQLite results"
25
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163 from_work_dir="db_with_spectral_matching.sqlite" >
0
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164 <filter>create_new_database is True</filter>
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165 </data>
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166 <data name="scan_hits" format="tsv" label="${tool.name} on ${on_string}: scan hits"
5
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167 from_work_dir="scan_hits.tsv" />
0
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168 <data name="xcms_hits" format="tsv" label="${tool.name} on ${on_string}: xcms hits"
5
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169 from_work_dir="xcms_hits.tsv" />
0
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170 </outputs>
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171 <tests>
5
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172 <test>
0
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173
5
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174 <param name="target_db" value="alldata.sqlite" />
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175 <output name="xcms_hits" value="xcms_hits.tsv" />
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176 <output name="scan_hits" value="scan_hits.tsv" />
0
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177
5
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178 </test>
0
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179 </tests>
5
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180
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181
0
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182 <help><![CDATA[
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183 =============================================================
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184 Spectral matching
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185 =============================================================
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186 -----------
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187 Description
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188 -----------
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190 Tool to perform spectral matching of MS/MS scans against library spectra
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192 The data inputs are:
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194 * library_db: An SQLite database of library ms/ms spectra (e.g. massbank, lipidsearch)
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195 * target_db: An SQLite database of the target ms/ms spectra (e.g. the data collected for an experiment)
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196
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197 The library spectra defaults to an SQLite database containing massbank and lipidsearch spectra. This can be downloaded and
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198 updated with your own spectra. Downloaded from:
0
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200 * https://www.dropbox.com/s/csxj6pairsgd8fe/library_spectra.db?dl=1
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201 * (more official location) https://bioconductor.org/packages/release/data/experiment/src/contrib/msPurityData_1.6.0.tar.gz
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203 The target_db can be generated from the frag4feature galaxy tool but will accept any SQLite database in the same format.
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205 See Bioconductor documentation for more details, function msPurity::spectral_matching().
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207 -----------
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208 Outputs
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209 -----------
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210 If the 'create_new_db', a copy of the target_db will be created that will now including spectral matching results
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211 spectra. Otherwise the original SQLite database will be updpated
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213 * scan_hits: All spectral matching hits for every scan
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214 * xcms_hits: All spectral matching hits that can be linked to an XCMS grouped feature
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215 * sqlite_results (if create_new_db==True): SQLite database of all data including spectral matching results
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218 ]]></help>
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220 <expand macro="citations"> </expand>
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221 </tool>