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annotate frag4feature.xml @ 9:174a523cb1da draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
author computational-metabolomics
date Thu, 13 Jun 2024 11:42:28 +0000
parents ab65999a5430
children
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ab65999a5430 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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1 <tool id="mspurity_frag4feature" name="msPurity.frag4feature" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
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2 <description>
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3 Assign fragmentation spectra to XCMS features using msPurity
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 Rscript '$__tool_directory__/frag4feature.R'
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11 --out_dir=.
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12 --xset='$xset'
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13 --pa='$pa'
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14 --cores=\${GALAXY_SLOTS:-4}
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15 #if $file_load_conditional.file_load_select=="yes"
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16 --mzML_files='
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17 #for $i in $file_load_conditional.input
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18 $i,
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19 #end for
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20 '
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21 --galaxy_names='
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22 #for $i in $file_load_conditional.input
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23 $i.name,
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24 #end for
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25 '
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26 #end if
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27 #if $useGroup
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28 --useGroup
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29 #end if
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30
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31 --ppm=$ppm
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32 --plim=$plim
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33 #if $intense
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34 --intense
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35 #end if
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36 #if $convert2RawRT
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37 --convert2RawRT
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38 #end if
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39
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40
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41 ]]></command>
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42 <inputs>
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43
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44 <param argument="--xset" type="data" label="xcmsSet object"
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45 help="grouped xcmsSet object saved as 'xset' in an RData file"
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46 format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata"/>
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47 <param argument="--pa" type="data" label="purityA object" format="rdata"
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48 help="purityA object generated from msPurity_purityA.
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49 Contains details of fragmentation spectra and precursor ion purity results
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50 (output from purityA tool)"/>
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51 <param argument="--ppm" type="float" value="10"
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52 label="ppm error tolerance between precursor mz and XCMS feature mz"
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53 help="Fragmentation will be ignored if the precursor mz value is not within
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54 the ppm error tolerance to the XCMS feature mz"/>
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55 <param argument="--plim" type="float" label="Precursor ion purity threshold"
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56 value="0" max="1" min="0"
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57 help="Fragmentation will be ignore if the precursor ion purity is less than the
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58 threshold (further filtering on the precursor ion purity can be done at the averaging
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59 stage if required)."/>
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60 <param argument="--intense" type="boolean" checked="true"
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61 label="Should the most intense precursor be used within the isolation window?"
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62 help="If TRUE the most intense precursor will be used. If FALSE the precursor
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63 closest to the center of the isolation window will be used"/>
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64 <param argument="--convert2RawRT" type="boolean" checked="false"
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65 label="Was retention time correction used?"
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66 help="If retention time correction has been used in XCMS set this to yes"/>
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67 <param argument="--useGroup" type="boolean" checked="false"
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68 label="For matching fragmentation to a feature, use the grouped feature range"
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69 help="For special cases where the MS2 files have no MS1 data or if the MS1 data in the MS2 file is unreliable" />
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70
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71 <expand macro="fileload" />
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72
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73 </inputs>
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74 <outputs>
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75 <data name="frag4feature_output_tsv" format="tsv" label="${tool.name} on ${on_string}: tsv"
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76 from_work_dir="frag4feature_output.tsv" />
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77 <data name="frag4feature_output_rdata" format="rdata" label="${tool.name} on ${on_string}: RData"
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78 from_work_dir="frag4feature_output.RData" />
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79 </outputs>
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80 <tests>
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81 <test>
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82 <conditional name="file_load_conditional">
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83 <param name="file_load_select" value="yes"/>
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84 <param name="input" >
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85 <collection type="list">
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86 <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
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87 <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
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88 <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
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89 <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
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90 </collection>
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91 </param>
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92 </conditional>
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93 <param name="xset" value="xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData"/>
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94 <param name="pa" value="purityA_output.RData"/>
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95 <output name="frag4feature_output_tsv" value="frag4feature_output.tsv"/>
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96 <output name="frag4feature_output_rdata" value="frag4feature_output.RData" ftype="rdata" compare="sim_size"/>
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97 </test>
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98 </tests>
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99
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100 <help><![CDATA[
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101 =============================================================
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102 Link fragmentation spectra to XCMS features
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103 =============================================================
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104 -----------
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105 Description
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106 -----------
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107
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108 **General**
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109
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110 Tool to Assign fragmentation spectra (MS/MS) stored within a purityA class object to grouped features within an XCMS xset object.
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111
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112 Please note that the xcmsSet object needs to have been grouped.
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113
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114 The data inputs are:
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115
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116 * A purityA object (generated from purityA) saved in an rdata file.
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117 * A xcmsSet grouped object (generated from xcms_group) saved in an rdata file
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118 * [optional] a dataset collection of the mzML files to resubmit
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119
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120 XCMS calculates individual chromatographic peaks for each mzML file (saved in xset@peaks), these are then grouped together
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121 (using xcms.group). Ideally the mzML files that contain the MS/MS spectra also contain sufficient MS1 scans for XCMS to detect
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122 MS1 chromatographic features. If this is the case, to determine if a MS2 spectra is to be linked to an XCMS grouped feature,
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123 the associated acquisition time of the MS/MS event has to be within the retention time window defined for the individual peaks
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124 associated for each file. The precursor m/z value also has to be within the user ppm tolerance to XCMS feature.
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125
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126 See below for representation of the linking (the \*------\* represent a many-to-many relationship) e.g. 1 or more MS/MS events can be
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127 linked to 1 or more individual feature and an individual XCMS feature can be linked to 1 or more grouped XCMS features
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128
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129 * \[grouped XCMS feature - across files\] \*------\* \[individual XCMS feature - per file\] \*------\* \[MS/MS spectra\]
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130
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131 Alternatively, if the "useGroup" argument is set to TRUE, the full width of the grouped peak (determined as the minimum rtmin
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132 and maximum rtmax of the all associated individual peaks) will be used. This option should be used if the mzML file with
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133 MS/MS has very limited MS1 data and so individual chromatographic peaks might not be detected with the mzML files containing the
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134 MS/MS data. However, it should be noted this may lead to potential inaccurate linking.
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135
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136 * \[grouped XCMS peaks\] \*------\* \[MS/MS spectra\]
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137
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138 **Example LC-MS/MS processing workflow**
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139
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140
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141 * Purity assessments
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142 + (mzML files) -> purityA -> (pa)
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143 * XCMS processing
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144 + (mzML files) -> xcms.xcmsSet -> xcms.merge -> xcms.group -> xcms.retcor -> xcms.group -> (xset)
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145 * Fragmentation processing
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146 + (xset, pa) -> **frag4feature** -> filterFragSpectra -> averageAllFragSpectra -> createDatabase -> spectralMatching -> (sqlite spectral database)
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147
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148 **Additional notes**
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149
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150 * If using only a single file, then grouping still needs to be performed within XCMS before frag4feature can be used.
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151 * Fragmentation spectra below a certain precursor ion purity can be be removed (see plim argument).
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152 * A SQLite database can be created directly here but the functionality has been deprecated and the createDatabase function should now be used
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153 * Can experience some problems when using XCMS version < 3 and obiwarp retention time correction.
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154
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155 See Bioconductor documentation for more details, function msPurity::frag4feature()
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156
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157 -----------
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158 Outputs
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159 -----------
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160 * frag4feature_rdata: An updated purityA object saved as rdata file with fragmentation-feature links added
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161 * frag4feature_grouped_msms: A flat file of all the XCMS peaks for each grouped feature and the corresponding fragmentation scans
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162 * frag4feature_sqlite: An SQLite database of the data (including fragmentation scans)
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163
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164 ]]></help>
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165
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166 <expand macro="citations" />
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167
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168 </tool>