Mercurial > repos > tomnl > mspurity_filterfragspectra

annotate filterFragSpectra.xml @ 9:82e94c75e5d6 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 116f938ddf39c78d7819fc62249bb11bf92cfcf1
author tomnl
date Tue, 25 Jun 2019 12:53:40 -0400
parents 43d4dd3288cd
children eeae5175cfed
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9
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1 <tool id="mspurity_filterfragspectra" name="msPurity.filterFragSpectra" version="0.2.4">
0
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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 </expand>
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10 <stdio>
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11 <exit_code range="1:" />
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12 </stdio>
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13 <command interpreter="Rscript"><![CDATA[
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14 filterFragSpectra.R
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15 --out_rdata=$filterFragSpectra_output_rdata
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16 --out_peaklist_prec=$filterFragSpectra_output_prec_tsv
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17 --out_peaklist_frag=$filterFragSpectra_output_frag_tsv
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18 --pa="$pa"
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19 --ilim=$ilim
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20 --plim=$plim
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21 --ra=$ra
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22 --snr=$snr
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23 --snmeth=$snmeth
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24 $rmp
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25 ]]></command>
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26 <inputs>
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27 <param name="pa" type="data"
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28 label="purityA object with fragmentation linked to XCMS features" format="rdata"
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29 help="purityA object saved as 'pa' in a RData file where fragmentation has
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30 been linked to XCMS features(output from frag4feature tool)"/>
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31 <param name="plim" type="float" value="0.5" help=""
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32 label="Miniumum precursor ion purity of the associated precursor for
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33 fragmentation spectra scan" />
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34 <param name="ilim" type="float" value="0.0" label="Peak instensity threshold" help="" />
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35 <param name="ra" type="float" min="0.0" max="1.0" value="0.0"
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36 label="Relative abundance threshold" help="" />
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37 <param name="snr" type="float" value="0.0" label="Signal-to-noise threshold" help="" />
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38 <param name="snmeth" type="select" label="Function to calculate noise." help="" >
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39 <option value="median" selected="true">median</option>
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40 <option value="mean">mean</option>
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41 <!-- <option value="mad">mad</option> -->
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42 </param>
4
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43 <param name="rmp" type="boolean" checked="false" truevalue="--rmp" falsevalue=""
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44 label="Remove peaks that do not meet the filtering criteria.
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45 Otherwise peaks will be flagged instead."
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46 help="" />
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47 </inputs>
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48 <outputs>
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49 <data name="filterFragSpectra_output_rdata" format="rdata"
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50 label="${tool.name} on ${on_string}: RData" />
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51 <data name="filterFragSpectra_output_prec_tsv" format="tsv"
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52 label="${tool.name} on ${on_string}: peaklist (precursors)" />
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53 <data name="filterFragSpectra_output_frag_tsv" format="tsv"
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54 label="${tool.name} on ${on_string}: peaklist (fragments)" />
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55 </outputs>
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56 <tests>
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57 <test>
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58 <param name="pa" value="frag4feature_output.RData" />
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59 <output name="filterFragSpectra_output_rdata"
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60 file="filterFragSpectra_output.RData" ftype="rdata" compare="sim_size" />
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61 <output name="filterFragSpectra_output_prec_tsv"
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62 file="filterFragSpectra_output_prec.tsv" ftype="tsv" />
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63 <output name="filterFragSpectra_output_frag_tsv"
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64 file="filterFragSpectra_output_frag.tsv" ftype="tsv" />
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65 </test>
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66 </tests>
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67
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68 <help><![CDATA[
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69 =============================================================
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70 Filter Fragmentation Spectra
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71 =============================================================
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72 -----------
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73 Description
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74 -----------
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75
1
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76 Flag and filter features based on signal-to-noise ratio, relative abundance, intensity threshold and precursor ion purity of precursor.
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77
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78
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79 **Example LC-MS/MS processing workflow**
0
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80
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81
1
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82 * Purity assessments
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83 + (mzML files) -> purityA -> (pa)
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84 * XCMS processing
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85 + (mzML files) -> xcms.xcmsSet -> xcms.merge -> xcms.group -> xcms.retcor -> xcms.group -> (xset)
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86 * Fragmentation processing
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87 + (xset, pa) -> frag4feature -> **filterFragSpectra** -> averageAllFragSpectra -> createDatabase -> spectralMatching -> (sqlite spectral database)
0
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88
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89 See Bioconductor documentation for more details, functions:
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90 msPurity::filterFragSpectra()
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91
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92 -----------
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93 Outputs
d6321d0e6efe planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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94 -----------
1
11f138472bb2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e67cf7a95ce430d1d373c03992a615da2f3eeeb1
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95 * filter_fragmentation_spectra_rdata: RData of the purityA object (pa) with filtered data
11f138472bb2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e67cf7a95ce430d1d373c03992a615da2f3eeeb1
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96 * peaklist_prec_tsv: precursor peaklist
11f138472bb2 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e67cf7a95ce430d1d373c03992a615da2f3eeeb1
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97 * peaklist_frag_tsv: fragmentation peaklist
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d6321d0e6efe planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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98
d6321d0e6efe planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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99 ]]></help>
d6321d0e6efe planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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100
d6321d0e6efe planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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101 <expand macro="citations" />
d6321d0e6efe planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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102
d6321d0e6efe planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
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103 </tool>