Mercurial > repos > computational-metabolomics > mspurity_averagefragspectra

annotate averageFragSpectra.xml @ 0:50eedf5ad217 draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
author computational-metabolomics
date Wed, 27 Nov 2019 13:35:22 -0500
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50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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1 <tool id="mspurity_averagefragspectra" name="msPurity.averageFragSpectra" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
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2 <description>Average and filter LC-MS/MS fragmentation spectra (Inter, Intra or All)</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 Rscript '$__tool_directory__/averageFragSpectra.R'
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9 --out_rdata='$averageFragSpectra_output_rdata'
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10 --out_peaklist='$averageFragSpectra_output_tsv'
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11 --pa='$pa'
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12 --av_level=$av_level
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13 --cores=\${GALAXY_SLOTS:-4}
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14 --minfrac=$minfrac
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15 --minnum=$minnum
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16 --ppm=$ppm
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17 --snr=$snr
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18 --ra=$ra
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19 --av=$av
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20 $sumi
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21 $rmp
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22 ]]></command>
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23 <inputs>
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24 <param argument="--pa" type="data" label="purityA object" format="rdata"
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25 help="purityA object saved as 'pa' in a RData file (output from frag4feature tool)"/>
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28 <param argument="--av_level" type="select" label="Average and filter fragmentation spectra for each XCMS feature" help="">
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29 <option value="intra" selected="true">within a MS data file</option>
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30 <option value="inter">across MS data files</option>
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31 <option value="all">within and across MS data files (ignoring intra and inter relationships)</option>
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32 </param>
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35 <param argument="--snr" type="float" min="0.0" value="0.0" label="Signal-to-noise threshold after averaging or summing" help="" />
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36 <param argument="--ra" type="float" min="0.0" max="1.0" value="0.0" label="Relative abundance threshold after averaging or summing" help="" />
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37 <param argument="--minfrac" type="float" min="0.0" max="1.0" value="0.5" label="Minimum fraction (i.e. percentage) of (averaged) scans a fragment peak has to be present in." help="" />
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38 <param argument="--minnum" type="integer" min="1" value="1" label="Minimum number of (averaged) fragmentation scans for a fragmentation event (precursor)." help="" />
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39 <param argument="--ppm" type="float" min="0.0" value="5.0" label="Ppm error tolerance" help="Maximum tolerated m/z deviation in parts per million." />
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40 <param argument="--sumi" type="boolean" checked="false" truevalue="--sumi" falsevalue="" label="Sum intensities across (averaged) scans?" help="" />
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41 <param argument="--av" type="select" label="Function to calculate the average intensity, m/z and SNR values across (averaged) scans after filtering." help="This is ignored for intensities when intensities are summed." >
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42 <option value="median" selected="true">median</option>
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43 <option value="mean">mean</option>
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44 </param>
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45
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46 <param argument="--rmp" type="boolean" checked="true" truevalue="--rmp" falsevalue="" label="Remove peaks that do not meet the filtering criteria. Otherwise peaks will be flagged instead."
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47 help="" />
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48 </inputs>
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49 <outputs>
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50 <data name="averageFragSpectra_output_rdata" format="rdata" label="${tool.name} (${av_level}) on ${on_string}: RData" />
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51 <data name="averageFragSpectra_output_tsv" format="tsv" label="${tool.name} (${av_level}) on ${on_string}: peaklist" />
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="av_level" value="intra" />
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56 <param name="pa" value="filterFragSpectra_output.RData" />
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57 <output name="averageFragSpectra_output_rdata" file="averageFragSpectra_output_intra.RData" ftype="rdata" compare="sim_size" />
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58 <output name="averageFragSpectra_output_tsv" file="averageFragSpectra_output_intra.tsv" ftype="tsv" />
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59 </test>
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60 <test>
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61 <param name="av_level" value="inter" />
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62 <param name="pa" value="averageFragSpectra_output_intra.RData" />
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63 <output name="averageFragSpectra_output_rdata" file="averageFragSpectra_output_inter.RData" ftype="rdata" compare="sim_size" />
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64 <output name="averageFragSpectra_output_tsv" file="averageFragSpectra_output_inter.tsv" ftype="tsv" />
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65 </test>
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66 <test>
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67 <param name="av_level" value="all" />
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68 <param name="pa" value="frag4feature_output.RData" />
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69 <output name="averageFragSpectra_output_rdata" file="averageFragSpectra_output_all_only.RData" ftype="rdata" compare="sim_size" />
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70 <output name="averageFragSpectra_output_tsv" file="averageFragSpectra_output_all_only.tsv" ftype="tsv" />
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71 </test>
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72 <test>
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73 <param name="av_level" value="all" />
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74 <param name="pa" value="averageFragSpectra_output_inter.RData" />
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75 <output name="averageFragSpectra_output_rdata" file="averageFragSpectra_output_all.RData" ftype="rdata" compare="sim_size" />
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76 <output name="averageFragSpectra_output_tsv" file="averageFragSpectra_output_all.tsv" ftype="tsv" />
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77
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78 </test>
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79 </tests>
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80
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81 <help><![CDATA[
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82 =============================================================
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83 Average Fragmentation Spectra
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84 =============================================================
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85 -----------
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86 Description
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87 -----------
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88
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89 Average and filter fragmentation spectra for each XCMS feature using an msPurity purityA object.
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90
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91 The tool uses the msPurity functions averageAllFragSpectra, averageIntraFragSpectra and
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92 averageInterFragSpectra.
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93
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94 The fragmentation spectra can be averaged in multiple ways; intra will average fragmentation
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95 spectra within an mzML file, inter will average fragmentation spectra across mzML files
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96 (requires intra to be run first) and all will average all spectra ignoring the intra and
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97 inter relationships.
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98
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99 The averaging is performed using hierarchical clustering of the m/z values of each peaks,
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100 where m/z values within a set ppm tolerance will be clustered. The clustered peaks are then
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101 averaged (or summed).
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102
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103 The fragmentation can be filtered on the averaged spectra (with the arguments snr, rsd, minfrac, ra)
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104
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105
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106 See Bioconductor documentation for more details, functions:
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107 msPurity::averageIntraFragSpectra()
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108 msPurity::averageInterFragSpectra()
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109 msPurity::averageAllFragSpectra()
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110
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111 -----------
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112 Outputs
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113 -----------
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114 * average_x_fragmentation_spectra_rdata
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115
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116 ]]></help>
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117
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118 <expand macro="citations" />
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119
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120 </tool>