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annotate FCSflowAI.xml @ 3:dd00eee6cd06 draft default tip

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planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
author azomics
date Fri, 29 Sep 2023 07:19:30 +0000
parents fab7c5deeb65
children
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3
dd00eee6cd06 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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1 <tool id="flowAI" name="flowAI" version="1.0+galaxy2">
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>
3
dd00eee6cd06 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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6 <requirement type="package" version="0.0.1">mscorefonts</requirement>
1
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7 </requirements>
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8 <stdio>
2
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9 <exit_code range="1:" level="fatal" description="See stderr for more details."/>
1
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10 </stdio>
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11 <command><![CDATA[
2
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12 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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13 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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14 #if $highQ_FCS:
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15 && cp high.fcs $highfcs
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16 #end if
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17 #if $lowQ_FCS:
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18 && cp low.fcs $lowfcs
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19 #end if
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20 #if $QC_FCS:
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21 && cp qc.fcs $qcfcs
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22 #end if
1
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23 ]]>
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24 </command>
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25 <inputs>
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26 <param format="fcs" name="input" type="data" label="FCS file"/>
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27 <param name="remove" type="select" label="Remove low quality cells from:">
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28 <option value="all">Flow rate, Signal acquisition and Dynamic range</option>
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29 <option value="FR_FS">Flow rate and Signal acquisition</option>
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30 <option value="FR_FM">Flow rate and Dynamic range</option>
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31 <option value="FS_FM">Signal acquisition and Dynamic range</option>
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32 <option value="FR">Flow rate</option>
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33 <option value="FS">Signal acquisition</option>
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34 <option value="FM">Dynamic range</option>
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35 </param>
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36 <param name="alphaFR" type="float" label="Significance threshold for flow rate check:" value="0.01"/>
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37 <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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38 <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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39 <param name="penFS" type="integer" label="Stringency of signal acquisition check (higher tolerance with higher values):" value="200"/>
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40 <param name="sideFM" type="select" label="Include in dynamic range check:">
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41 <option value="both">Both limits</option>
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42 <option value="upper">Upper limit only</option>
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43 <option value="lower">Lower limit only</option>
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44 </param>
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45 <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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46 <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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47 <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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48 </inputs>
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49 <outputs>
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50 <data format="html" name="full_rep" label="QC of ${input.name}">
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51 </data>
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52 <data format="fcs" name="highfcs" label="High quality events only from ${input.name}">
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53 <filter>(highQ_FCS)</filter>
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54 </data>
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55 <data format="fcs" name="lowfcs" label="Low quality events only from ${input.name}">
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56 <filter>(lowQ_FCS)</filter>
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57 </data>
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58 <data format="fcs" name="qcfcs" label="All events (low quality event marked up) from ${input.name}">
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59 <filter>(QC_FCS)</filter>
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60 </data>
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61 </outputs>
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62 <tests>
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63 <test expect_num_outputs="2">
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64 <param name="input" value="input.fcs"/>
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65 <param name="remove" value="all"/>
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66 <param name="alphaFR" value="0.01"/>
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67 <param name="chremFS" value="TRUE"/>
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68 <param name="outFS" value="FALSE"/>
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69 <param name="penFS" value="200"/>
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70 <param name="sideFM" value="both"/>
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71 <param name="highQ_FCS" value="TRUE"/>
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72 <param name="lowQ_FCS" value="FALSE"/>
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73 <param name="QC_FCS" value="FALSE"/>
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74 <output name="full_rep">
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75 <assert_contents>
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76 <has_n_lines min="100" max="500"/>
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77 <has_text text="data:image/png;base64"/>
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78 <has_text text="Dynamic range check"/>
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79 <has_text text="total_UNIQUE"/>
3
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80 <has_size value="320266" delta="30000"/>
2
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81 </assert_contents>
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82 </output>
1
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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83 <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"
azomics
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diff changeset
84 </test>
2
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
azomics
parents: 1
diff changeset
85 <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
86 <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
87 <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
88 <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
89 <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
90 <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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91 <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
92 <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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93 <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
94 <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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diff changeset
95 <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
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96 <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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97 <assert_contents>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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98 <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
azomics
parents: 1
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99 <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
parents: 1
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100 <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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101 <has_text text="total_UNIQUE"/>
3
dd00eee6cd06 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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102 <has_size value="320266" delta="30000"/>
2
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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103 </assert_contents>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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104 </output>
1
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="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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106 <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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107 <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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108 </test>
2
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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109 <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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110 <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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111 <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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112 <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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113 <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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114 <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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115 <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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116 <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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117 <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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118 <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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119 <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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120 <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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121 <assert_contents>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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122 <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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123 <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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124 <has_text text="Dynamic range check"/>
3
dd00eee6cd06 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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125 <has_size value="320433" delta="30000"/>
2
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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126 </assert_contents>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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127 </output>
1
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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128 <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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129 </test>
2
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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130 <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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131 <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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132 <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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133 <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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134 <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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135 <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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136 <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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137 <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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138 <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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139 <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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140 <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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141 <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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142 <assert_contents>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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143 <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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parents: 1
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144 <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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145 <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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146 <has_text text="total_UNIQUE"/>
3
dd00eee6cd06 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit bbff20e20dc2b9dbb40b613a0d5f16ee8132446d
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147 <has_size value="320220" delta="30000"/>
2
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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148 </assert_contents>
fab7c5deeb65 planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 2482f9499096cc780cf1bf688ea07de150191be5
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149 </output>
1
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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150 <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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151 </test>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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152 </tests>
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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153 <help><![CDATA[
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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154 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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155
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
azomics
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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
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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158 **Input files**
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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159
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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160 • 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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161
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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162 **Output files**
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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163
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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164 • 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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165 • 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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166 • 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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167 • 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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168
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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169
34397a84faf1 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowai commit 83ef47729f2d2cdae84171761a6795df9fb63389"
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170 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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172 ----
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173
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174 Description of the approach
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175 '''''''''''''''''''''''''''
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176 This tool identifies anomalies from three fundamental properties of flow cytometry data:
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177
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178 - *Flow rate*. Surges and substantial shifts of the rate of the cells passing through the capillary tube are detected.
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179
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180 - *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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181
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182 - *Dynamic range*. Values recorded in the upper limit (margin events) and negative outliers are removed.
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183
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184 .. class:: infomark
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185
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186 An HTML report with informative plots is generated. Users are advised to review the report and also::
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187
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188 1. Eventually adjust the quality control parameters
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189 2. Discard the entire FCS file because of an unacceptable number of anomalies
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190 3. Program a flow cytometry maintenance because of recurrent issues
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191
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192
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193 Parameters
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194 ''''''''''
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195 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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196
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197 Example
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198 '''''''
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199 This section provides an example of a flowAI quality control html report with plots:
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200
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201
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202 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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203
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204 .. image:: ./static/images/flowtools/autoflowrate.png
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205
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206 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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207
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208 .. image:: ./static/images/flowtools/autosignal.png
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209
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210 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
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212 .. image:: ./static/images/flowtools/margins.png
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214 ]]>
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215 </help>
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216 <citations>
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217 <citation type="doi">10.1093/bioinformatics/btw191</citation>
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218 </citations>
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219 </tool>