Mercurial > repos > immport-devteam > flowai

annotate FCSflowAI.xml @ 2:fab7c5deeb65 draft

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planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
author azomics
date Tue, 26 Sep 2023 23:19:04 +0000
parents 34397a84faf1
children dd00eee6cd06
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fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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1 <tool id="flowAI" name="flowAI" version="1.0+galaxy1">
1
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2 <description> automatic quality control</description>
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3 <requirements>
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4 <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement>
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5 <requirement type="package" version="1.2.9">bioconductor-flowai</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" level="fatal" description="See stderr for more details."/>
1
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9 </stdio>
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10 <command><![CDATA[
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11 Rscript $__tool_directory__/FCSflowAI.R '${input}' '${remove}' $alphaFR $chremFS $outFS $penFS '${sideFM}' report.html high.fcs low.fcs qc.fcs &&
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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12 cp report.html $full_rep
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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13 #if $highQ_FCS:
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14 && cp high.fcs $highfcs
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15 #end if
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16 #if $lowQ_FCS:
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17 && cp low.fcs $lowfcs
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18 #end if
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19 #if $QC_FCS:
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20 && cp qc.fcs $qcfcs
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21 #end if
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22 ]]>
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23 </command>
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24 <inputs>
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25 <param format="fcs" name="input" type="data" label="FCS file"/>
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26 <param name="remove" type="select" label="Remove low quality cells from:">
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27 <option value="all">Flow rate, Signal acquisition and Dynamic range</option>
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28 <option value="FR_FS">Flow rate and Signal acquisition</option>
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29 <option value="FR_FM">Flow rate and Dynamic range</option>
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30 <option value="FS_FM">Signal acquisition and Dynamic range</option>
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31 <option value="FR">Flow rate</option>
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32 <option value="FS">Signal acquisition</option>
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33 <option value="FM">Dynamic range</option>
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34 </param>
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35 <param name="alphaFR" type="float" label="Significance threshold for flow rate check:" value="0.01"/>
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36 <param name="chremFS" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Do you want to exclude the FSC and SSC parameters from the signal acquisition check?" help="The FSC and SSC parameters will not be taken into account for analysis but will not be removed."/>
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37 <param name="outFS" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Do you want to remove outliers before the signal acquisition check?"/>
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38 <param name="penFS" type="integer" label="Stringency of signal acquisition check (higher tolerance with higher values):" value="200"/>
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39 <param name="sideFM" type="select" label="Include in dynamic range check:">
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40 <option value="both">Both limits</option>
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41 <option value="upper">Upper limit only</option>
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42 <option value="lower">Lower limit only</option>
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43 </param>
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44 <param name="highQ_FCS" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Create FCS file with only high quality events?"/>
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45 <param name="lowQ_FCS" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Create FCS file with only low quality events?"/>
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46 <param name="QC_FCS" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Create FCS file with an additional parameter where low quality events have values higher than 10,000?"/>
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47 </inputs>
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48 <outputs>
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49 <data format="html" name="full_rep" label="QC of ${input.name}">
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50 </data>
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51 <data format="fcs" name="highfcs" label="High quality events only from ${input.name}">
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52 <filter>(highQ_FCS)</filter>
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53 </data>
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54 <data format="fcs" name="lowfcs" label="Low quality events only from ${input.name}">
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55 <filter>(lowQ_FCS)</filter>
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56 </data>
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57 <data format="fcs" name="qcfcs" label="All events (low quality event marked up) from ${input.name}">
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58 <filter>(QC_FCS)</filter>
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59 </data>
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60 </outputs>
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61 <tests>
2
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62 <test expect_num_outputs="2">
1
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63 <param name="input" value="input.fcs"/>
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64 <param name="remove" value="all"/>
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65 <param name="alphaFR" value="0.01"/>
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66 <param name="chremFS" value="TRUE"/>
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67 <param name="outFS" value="FALSE"/>
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68 <param name="penFS" value="200"/>
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69 <param name="sideFM" value="both"/>
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70 <param name="highQ_FCS" value="TRUE"/>
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71 <param name="lowQ_FCS" value="FALSE"/>
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72 <param name="QC_FCS" value="FALSE"/>
2
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73 <output name="full_rep">
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74 <assert_contents>
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75 <has_n_lines min="100" max="500"/>
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76 <has_text text="data:image/png;base64"/>
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77 <has_text text="Dynamic range check"/>
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78 <has_text text="total_UNIQUE"/>
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79 <has_size value="267939" delta="30000"/>
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80 </assert_contents>
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81 </output>
1
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82 <output name="highfcs" file="std/hqdata.fcs" compare="sim_size"/>
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83 </test>
2
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84 <test expect_num_outputs="4">
1
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
azomics
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diff changeset
85 <param name="input" value="input.fcs"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
azomics
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diff changeset
86 <param name="remove" value="all"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
azomics
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diff changeset
87 <param name="alphaFR" value="0.01"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
azomics
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diff changeset
88 <param name="chremFS" value="TRUE"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
azomics
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diff changeset
89 <param name="outFS" value="FALSE"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
azomics
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diff changeset
90 <param name="penFS" value="200"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
azomics
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diff changeset
91 <param name="sideFM" value="both"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
azomics
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diff changeset
92 <param name="highQ_FCS" value="TRUE"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
azomics
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diff changeset
93 <param name="lowQ_FCS" value="TRUE"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
azomics
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94 <param name="QC_FCS" value="TRUE"/>
2
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
azomics
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95 <output name="full_rep">
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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96 <assert_contents>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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97 <has_n_lines min="100" max="500"/>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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98 <has_text text="data:image/png;base64"/>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
azomics
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99 <has_text text="Dynamic range check"/>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
azomics
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100 <has_text text="total_UNIQUE"/>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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101 <has_size value="267939" delta="30000"/>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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102 </assert_contents>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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103 </output>
1
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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104 <output name="highfcs" file="std/hqdata.fcs" compare="sim_size"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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105 <output name="lowfcs" file="std/lqdata.fcs" compare="sim_size"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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106 <output name="qcfcs" file="std/alldata.fcs" compare="sim_size"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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107 </test>
2
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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108 <test expect_num_outputs="2">
1
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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diff changeset
109 <param name="input" value="input.fcs"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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110 <param name="remove" value="all"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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diff changeset
111 <param name="alphaFR" value="0.01"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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diff changeset
112 <param name="chremFS" value="TRUE"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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diff changeset
113 <param name="outFS" value="TRUE"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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114 <param name="penFS" value="200"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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diff changeset
115 <param name="sideFM" value="both"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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116 <param name="highQ_FCS" value="TRUE"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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117 <param name="lowQ_FCS" value="FALSE"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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118 <param name="QC_FCS" value="FALSE"/>
2
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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119 <output name="full_rep">
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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120 <assert_contents>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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121 <has_n_lines min="100" max="500"/>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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122 <has_text text="data:image/png;base64"/>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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123 <has_text text="Dynamic range check"/>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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124 <has_size value="268106" delta="30000"/>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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125 </assert_contents>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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126 </output>
1
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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127 <output name="highfcs" file="nooutliers/hqdata_nooutliers.fcs" compare="sim_size"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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128 </test>
2
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129 <test expect_num_outputs="2">
1
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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130 <param name="input" value="input.fcs"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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131 <param name="remove" value="all"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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132 <param name="alphaFR" value="0.01"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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133 <param name="chremFS" value="FALSE"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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134 <param name="outFS" value="FALSE"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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135 <param name="penFS" value="200"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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136 <param name="sideFM" value="both"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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137 <param name="highQ_FCS" value="TRUE"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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138 <param name="lowQ_FCS" value="FALSE"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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139 <param name="QC_FCS" value="FALSE"/>
2
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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140 <output name="full_rep">
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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141 <assert_contents>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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142 <has_n_lines min="100" max="500"/>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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143 <has_text text="data:image/png;base64"/>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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144 <has_text text="Dynamic range check"/>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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145 <has_text text="total_UNIQUE"/>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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146 <has_size value="267894" delta="30000"/>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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147 </assert_contents>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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148 </output>
1
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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149 <output name="highfcs" file="withsfsc/hqdata_sfsc.fcs" compare="sim_size"/>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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150 </test>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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151 </tests>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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152 <help><![CDATA[
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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153 This tool automatically performs quality control of flow cytometry data.
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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154
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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155 -----
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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156
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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157 **Input files**
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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158
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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159 • One or more FCS files.
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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160
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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161 **Output files**
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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162
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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163 • full HTML report
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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164 • new FCS file containing only high quality events (default)
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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165 • new FCS file containing only low quality events (optional)
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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166 • original FCS file containing an additional parameter where the low quality events have a value higher than 10,000 (optional)
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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167
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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168
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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169 The files generated will be FCS 3.0.
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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170
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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171 ----
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173 Description of the approach
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174 '''''''''''''''''''''''''''
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175 This tool identifies anomalies from three fundamental properties of flow cytometry data:
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176
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177 - *Flow rate*. Surges and substantial shifts of the rate of the cells passing through the capillary tube are detected.
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178
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179 - *Signal acquisition*. Instability in the signal acquired for each channel are detected. In most cases it corresponds to flow rate surges and shifts.
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180
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181 - *Dynamic range*. Values recorded in the upper limit (margin events) and negative outliers are removed.
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182
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183 .. class:: infomark
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184
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185 An HTML report with informative plots is generated. Users are advised to review the report and also::
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186
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187 1. Eventually adjust the quality control parameters
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188 2. Discard the entire FCS file because of an unacceptable number of anomalies
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189 3. Program a flow cytometry maintenance because of recurrent issues
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190
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191
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192 Parameters
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193 ''''''''''
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194 Default settings work well in the majority of cases. Setting customization may be needed to address properties of unique datasets. For example, high-dimensional FCS files may perform best with more tolerant setttings for signal acquisition checks.
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195
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196 Example
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197 '''''''
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198 This section provides an example of a flowAI quality control html report with plots:
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199
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200
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201 Flow rate check: anomalies are flagged with a green circle. In this instance a surge was detected and discarded as well as a shift from the median value later in the experiment.
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202
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203 .. image:: ./static/images/flowtools/autoflowrate.png
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204
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205 Signal acquistion check: Orange background (or yellow depending on the user's computer) highlights the stable region. Signal acquistion shifts are identified on a per channel basis and the largest region containing no anomalies is retained.
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206
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207 .. image:: ./static/images/flowtools/autosignal.png
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209 Dynamic range check: red and blue lines reflect the detected number of events over time. The x-axis corresponds to that of the signal acquisition plot.
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211 .. image:: ./static/images/flowtools/margins.png
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213 ]]>
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214 </help>
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215 <citations>
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216 <citation type="doi">10.1093/bioinformatics/btw191</citation>
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217 </citations>
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218 </tool>