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1 <tool id="auto_collapse_populations" name="Collapse populations automatically" version="1.0">
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2 <description>based on quartile binning from FLOCK results.</description>
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3 <requirements>
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4 <requirement type="package" version="0.17.1">pandas</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <command><![CDATA[
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10 python $__tool_directory__/auto_collapse_pops.py -o "${output}" -i "${input}" -p "${profile}" -r "${report}"
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11 ]]>
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12 </command>
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13 <inputs>
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14 <param format="flowclr" name="input" type="data" label="FLOCK or Cross-Sample output file"/>
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15 <param format="flowscore" name="profile" type="data" label="Population score profiles from FLOCK"/>
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16 </inputs>
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17 <outputs>
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18 <data format="flowclr" name="output" label="Auto-collapsed pops in ${input.name}"/>
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19 <data format="tabular" name="report" label="Auto-collapse report for ${input.name} with ${profile.name}"/>
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="input" value="input.flowclr"/>
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24 <param name="profile=" value="profile.flowscore"/>
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25 <param name="report" value="report.txt"/>
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26 <output name="output" file="output.flowclr"/>
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27 </test>
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28 </tests>
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29 <help><![CDATA[
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30 This tool automatically collapses populations together based on FLOCK score profiles.
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31
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32 -----
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33
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34 .. class:: warningmark
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35
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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*
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37
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38 -----
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39
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40 **Input**
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41
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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.
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43
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44 **Output**
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45
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46 The input file with selected populations replaced by the indicated population. This tool also generates a report.
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47
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48 -----
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49
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50 **Example**
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51
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52 *Input* - fluorescence intensities per marker and population ID per event::
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53
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54 Marker1 Marker2 Marker3 Population
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55 34 45 12 1
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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
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59
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60 *Population profile file*::
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61
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62 Population_ID Marker1 Marker2 Marker3 Count Percentage
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63 1 2 2 3 3885 6.44
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64 2 1 3 4 2774 4.62
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65 3 2 2 3 2151 3.59
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66 4 1 3 2 1207 2.01
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67
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68 *Output* - fluorescence intensities per marker and population ID per event::
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69
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70 Marker1 Marker2 Marker3 Population
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71 34 45 12 1
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72 33 65 10 4
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73 19 62 98 2
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74 12 36 58 1
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75
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76 *Output* - fluorescence intensities per marker and population ID per event::
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77
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78 New_Population Former_Populations Marker1 Marker2 Marker3
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79 1 1, 3 2 2 3
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80 2 2 1 3 4
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81 3 4 1 3 2
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82 4 5, 8, 12 3 1 1
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83 ]]>
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84 </help>
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85 </tool>
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