Mercurial > repos > immport-devteam > auto_collapse_pop

annotate auto_collapse_pops.xml @ 1:08b71aee9b80 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
author azomics
date Mon, 22 Jun 2020 17:22:03 -0400
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08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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1 <tool id="auto_collapse_populations" name="Collapse populations automatically" version="1.0+galaxy1">
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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2 <description>based on quartile binning from FLOCK results</description>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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3 <requirements>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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4 <requirement type="package" version="0.17.1">pandas</requirement>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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5 </requirements>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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6 <stdio>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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7 <exit_code range="1:" />
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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8 </stdio>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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9 <command><![CDATA[
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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10 python '$__tool_directory__/auto_collapse_pops.py' -o '${output}' -i '${input}' -p '${profile}' -r '${report}'
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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11 ]]>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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12 </command>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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13 <inputs>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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14 <param format="flowclr" name="input" type="data" label="FLOCK or Cross-Sample output file"/>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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15 <param format="flowscore" name="profile" type="data" label="Population score profiles from FLOCK"/>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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16 </inputs>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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17 <outputs>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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18 <data format="flowclr" name="output" label="Auto-collapsed pops in ${input.name}"/>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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19 <data format="tabular" name="report" label="Auto-collapse report for ${input.name} with ${profile.name}"/>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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20 </outputs>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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21 <tests>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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22 <test>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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23 <param name="input" value="input.flowclr"/>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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24 <param name="profile" value="profile.flowscore"/>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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25 <param name="report" value="report.txt"/>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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26 <output name="output" file="output.flowclr" compare="sim_size"/>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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27 </test>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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28 </tests>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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29 <help><![CDATA[
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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30 This tool automatically collapses populations together based on FLOCK score profiles.
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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32 -----
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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34 .. class:: warningmark
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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36 *FLOCK score profiles are assigned based on quartile binning of the data. As always, use this tool with caution and be critical of your results*
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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38 -----
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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40 **Input**
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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42 FLOCK or Cross Sample output - a table of the fluorescence intensities for each event and the population associated with each, as well as the file containing the score profiles for each FLOCK population.
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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43
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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44 **Output**
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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45
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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46 The input file with selected populations replaced by the indicated population. This tool also generates a report.
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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48 -----
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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50 **Example**
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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52 *Input* - fluorescence intensities per marker and population ID per event::
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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54 Marker1 Marker2 Marker3 ... Population
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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55 34 45 12 ... 1
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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56 33 65 10 ... 5
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57 19 62 98 ... 2
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58 12 36 58 ... 3
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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59 ... ... ... ... ...
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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61 *Population profile file*::
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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63 Population_ID Marker1 Marker2 Marker3 ... Count Percentage
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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64 1 2 2 3 ... 3885 6.44
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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65 2 1 3 4 ... 2774 4.62
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66 3 2 2 3 ... 2151 3.59
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67 4 1 3 2 ... 1207 2.01
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68 ... ... ... ... ... ... ...
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08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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70 *Output* - fluorescence intensities per marker and population ID per event::
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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72 Marker1 Marker2 Marker3 ... Population
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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73 34 45 12 ... 1
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75 19 62 98 ... 2
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08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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79 *Output* - fluorescence intensities per marker and population ID per event::
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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81 New_Population Former_Populations Marker1 Marker2 Marker3 ...
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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82 1 1, 3 2 2 3 ...
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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84 3 4 1 3 2 ...
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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85 4 5, 8, 12 3 1 1 ...
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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87 ]]>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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88 </help>
08b71aee9b80 "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/auto_collapse_pop commit c4cd54a5b7a57f494a82d2a5e9b94f24473fff24"
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89 </tool>