Mercurial > repos > tomnl > cameradims
annotate cameradims.xml @ 20:8e33abdebc57 draft default tip
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 14435cfc042911bf1ee409f5a0d5ef908f5feec0-dirty
author | tomnl |
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date | Thu, 21 Jun 2018 11:28:11 -0400 |
parents | d4081e4160af |
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rev | line source |
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20
8e33abdebc57
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 14435cfc042911bf1ee409f5a0d5ef908f5feec0-dirty
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1 <tool id="cameradims" name="CAMERA_DIMS" version="0.2.6"> |
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55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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2 <description>Modification of the R package CAMERA to work on DIMS data</description> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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3 <requirements> |
20
8e33abdebc57
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 14435cfc042911bf1ee409f5a0d5ef908f5feec0-dirty
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4 <requirement type="package" version="0.2.9">r-cameradims</requirement> |
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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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5 </requirements> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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6 <stdio> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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7 <exit_code range="1:" /> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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8 </stdio> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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9 <command interpreter="Rscript"><![CDATA[ |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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10 cameradims.R --in_file $peaks_file |
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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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11 --out_dir . |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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12 --ppm_adduct $ppm_adduct |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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13 --ppm_iso $ppm_iso |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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14 --mzabs_adduct $mzabs_adduct |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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15 --mzabs_iso $mzabs_iso |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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16 --maxiso $maxiso |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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17 --maxcharge $maxcharge |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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18 --maxmol $maxmol |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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19 --polarity $polarity |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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20 --rule_type $ruleset.ruleset |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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21 #if $ruleset.ruleset == 'user' |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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22 --rule_path $ruleset.rulesfile |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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23 #end if |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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24 #if $export_ruleset |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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25 --export_ruleset |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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26 #end if |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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27 --intensity_filter=$intensity_filter |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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28 ]]></command> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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29 |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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30 <inputs> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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31 <param type="data" name="peaks_file" format="tabular,tsv" |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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32 help="tsv or tabular file with mz and intensity columns"/> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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33 <param name="ppm_adduct" type="float" label="ppm (adduct)" value="5" |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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34 help="general ppm error (adduct)"/> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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35 <param name="ppm_iso" type="float" label="ppm (iso)" value="5" |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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36 help="general ppm error (iso)"/> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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37 <param name="mzabs_adduct" type="float" label="mzabs (adduct)" value="0.015" |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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38 help="general absolute error in m/z"/> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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39 <param name="mzabs_iso" type="float" label="mzabs (iso)" value="0.015" |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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40 help="general absolute error in m/z"/> |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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41 <param name="maxmol" type="integer" label="maxmol" value="3" |
55aa2dd24828
planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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42 help="highest number(n) of allowed clusterion [nM+ion] (argument called multiplier in findAdducts())"/> |
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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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43 <param name="maxiso" type="integer" label="maxiso" value="4" |
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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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44 help="max number of expected isotopes"/> |
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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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45 <param name="maxcharge" type="integer" label="maxcharge" value="3" |
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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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46 help="max ion charge for finding isotopes"/> |
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47 <param name="polarity" type="select" label="polarity" help="Which polarity mode was used for measuring of the ms sample" > |
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48 <option value="pos" selected="true">positive</option> |
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49 <option value="neg">negative</option> |
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50 </param> |
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51 |
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52 <param name="intensity_filter" type="float" label="Intensity filter" value="5000" |
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53 help="Filter out any peaks that have intensity less than this value. (Adduct calculation may take |
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54 a very long time if peaks are not filtered before hand) "/> |
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55 |
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56 <conditional name="ruleset"> |
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57 <param name="ruleset" type="select" label="Rules for adducts" > |
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58 <option value="primary adducts" >Primary adducts ([M+Na]+, [M+K]+ and [M+NH4]+")</option> |
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59 <option value="extended" selected="true" >Extended adducts</option> |
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60 <option value="extended_large" >Extended adducts (large)</option> |
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61 <option value="user" >Provide a csv file of the rules to use</option> |
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62 </param> |
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63 <when value="user"> |
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64 <param type="data" name="rulesfile" format="tsv, tabular" |
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65 help="User supplied rules file used to to calculate adducts, should contain the following |
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66 columns name,nmol,charge,massdiff,oidscore,quasi,ips. |
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67 If using the adducts to guide fragmentation then the frag_score column should be included. Where |
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68 a score of 1 indicates the adduct is the best adduct form to fragment"/> |
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69 </when> |
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70 <when value="extended"> |
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71 </when> |
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72 <when value="primary adducts"> |
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73 </when> |
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74 </conditional> |
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75 <param name="export_ruleset" type="boolean" label="Export the adduct ruleset used?" help=""/> |
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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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76 </inputs> |
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77 <outputs> |
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78 <data name="camera_annotated_map" format="tsv" label="${tool.name} on ${on_string}: map" |
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79 from_work_dir="camera_annotated_map.txt" /> |
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80 <data name="camera_annotated_peaklist" label="${tool.name} on ${on_string}: peaklist" |
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81 from_work_dir="camera_annotated_peaklist.txt" format="tsv"/> |
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82 <data name="ruleset" label="${tool.name} on ${on_string}: ruleset" |
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planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 6c48bd51987a28401de6cf5e49b1b30e5e73fe16-dirty
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83 from_work_dir="ruleset.txt" format="tsv"> |
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84 <filter>export_ruleset is True</filter> |
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85 </data> |
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86 |
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87 |
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88 |
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89 </outputs> |
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90 <tests> |
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91 <test> |
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92 <param name="peaks_file" value="peaklist_in.tsv" ftype="tsv"/> |
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93 <output name="camera_annotated_peaklist" value="camera_annotated_peaklist.txt"/> |
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94 <output name="camera_annotated_map" value="camera_annotated_map.txt"/> |
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95 </test> |
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96 </tests> |
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97 <help><![CDATA[ |
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98 cameraDIMS |
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99 |
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100 ]]></help> |
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101 <citations> |
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102 <citation type="doi">10.1021/ac202450g</citation> |
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103 </citations> |
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104 </tool> |