Mercurial > repos > computational-metabolomics > mspurity_filterfragspectra

annotate filterFragSpectra.xml @ 3:cad0376c0b66 draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 89bf304d12233004031de3c3e703a472b0ba5459"
author computational-metabolomics
date Thu, 09 Apr 2020 14:28:45 -0400
parents 96af79da0cc6
children 2e10c13085c9
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96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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1 <tool id="mspurity_filterfragspectra" name="msPurity.filterFragSpectra" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
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2 <description>
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3 Filter fragmentations spectra associated with an XCMS feature
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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" interpreter="Rscript"><![CDATA[
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10 filterFragSpectra.R
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11 --out_rdata='$filterFragSpectra_output_rdata'
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12 --out_peaklist_prec='$filterFragSpectra_output_prec_tsv'
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13 --out_peaklist_frag='$filterFragSpectra_output_frag_tsv'
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14 --pa='$pa'
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15 --ilim=$ilim
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16 --plim=$plim
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17 --ra=$ra
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18 --snr=$snr
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19 --snmeth=$snmeth
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20 $rmp
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21 ]]></command>
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22 <inputs>
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23 <param argument="--pa" type="data"
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24 label="purityA object with fragmentation linked to XCMS features" format="rdata"
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25 help="purityA object saved as 'pa' in a RData file where fragmentation has
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26 been linked to XCMS features(output from frag4feature tool)"/>
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27 <param argument="--plim" type="float" value="0.5" help=""
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28 label="Miniumum precursor ion purity of the associated precursor for
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29 fragmentation spectra scan" />
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30 <param argument="--ilim" type="float" value="0.0" label="Peak instensity threshold" help="" />
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31 <param argument="--ra" type="float" min="0.0" max="1.0" value="0.0"
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32 label="Relative abundance threshold" help="" />
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33 <param argument="--snr" type="float" value="0.0" label="Signal-to-noise threshold" help="" />
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34 <param argument="--snmeth" type="select" label="Function to calculate noise." help="" >
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35 <option value="median" selected="true">median</option>
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36 <option value="mean">mean</option>
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37 <!-- <option value="mad">mad</option> -->
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38 </param>
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39 <param argument="--rmp" type="boolean" checked="false" truevalue="--rmp" falsevalue=""
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40 label="Remove peaks that do not meet the filtering criteria.
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41 Otherwise peaks will be flagged instead."
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42 help="" />
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43 </inputs>
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44 <outputs>
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45 <data name="filterFragSpectra_output_rdata" format="rdata"
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46 label="${tool.name} on ${on_string}: RData" />
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47 <data name="filterFragSpectra_output_prec_tsv" format="tsv"
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48 label="${tool.name} on ${on_string}: peaklist (precursors)" />
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49 <data name="filterFragSpectra_output_frag_tsv" format="tsv"
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50 label="${tool.name} on ${on_string}: peaklist (fragments)" />
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51 </outputs>
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52 <tests>
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53 <test>
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54 <param name="pa" value="frag4feature_output.RData" />
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55 <output name="filterFragSpectra_output_rdata"
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56 file="filterFragSpectra_output.RData" ftype="rdata" compare="sim_size" />
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57 <output name="filterFragSpectra_output_prec_tsv"
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58 file="filterFragSpectra_output_prec.tsv" ftype="tsv" />
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59 <output name="filterFragSpectra_output_frag_tsv"
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60 file="filterFragSpectra_output_frag.tsv" ftype="tsv" />
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61 </test>
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62 </tests>
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63
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64 <help><![CDATA[
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65 =============================================================
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66 Filter Fragmentation Spectra
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67 =============================================================
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68 -----------
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69 Description
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70 -----------
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71
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72 Flag and filter features based on signal-to-noise ratio, relative abundance, intensity threshold and precursor ion purity of precursor.
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73
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74
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75 **Example LC-MS/MS processing workflow**
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76
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77
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78 * Purity assessments
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79 + (mzML files) -> purityA -> (pa)
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80 * XCMS processing
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81 + (mzML files) -> xcms.xcmsSet -> xcms.merge -> xcms.group -> xcms.retcor -> xcms.group -> (xset)
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82 * Fragmentation processing
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83 + (xset, pa) -> frag4feature -> **filterFragSpectra** -> averageAllFragSpectra -> createDatabase -> spectralMatching -> (sqlite spectral database)
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84
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85 See Bioconductor documentation for more details, functions:
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86 msPurity::filterFragSpectra()
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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87
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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88 -----------
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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89 Outputs
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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90 -----------
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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91 * filter_fragmentation_spectra_rdata: RData of the purityA object (pa) with filtered data
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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92 * peaklist_prec_tsv: precursor peaklist
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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93 * peaklist_frag_tsv: fragmentation peaklist
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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94
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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95 ]]></help>
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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96
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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97 <expand macro="citations" />
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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98
96af79da0cc6 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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99 </tool>