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1 <tool id="generate_mfi" name="Generate the centroids" version="1.0">
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2 <description>from a flow result file</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 <requirement type="package" version="1.10.2">numpy</requirement>
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6 <requirement type="package" version="0.16.0">scipy</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1:" />
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10 </stdio>
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11 <command><![CDATA[
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12 python $__tool_directory__/generateMFI.py -i "${input}" -o "${output}" -M "${mfi}"
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13 ]]>
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14 </command>
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15 <inputs>
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16 <param format="flowclr" name="input" type="data" label="Flow Text file"/>
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17 <param name="mfi" type="select" label="Calculate centroids using:">
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18 <option value="mfi" selected="true">Mean Fluorescence Intensity</option>
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19 <option value="mdfi">Median Fluorescence Intensity</option>
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20 <option value="gmfi">Geometric Mean Fluorescence Intensity</option>
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21 </param>
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22 </inputs>
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23 <outputs>
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24 <data format="flowmfi" name="output" label="${mfi} centroids from ${input.name}"/>
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="input" value="input.flowclr"/>
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29 <param name="mfi" value="mfi"/>
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30 <output name="output" file="mfi.flowmfi"/>
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31 </test>
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32 <test>
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33 <param name="input" value="input.flowclr"/>
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34 <param name="mfi" value="mdfi"/>
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35 <output name="output" file="mdfi.flowmfi"/>
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36 </test>
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37 <test>
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38 <param name="input" value="input.flowclr"/>
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39 <param name="mfi" value="gmfi"/>
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40 <output name="output" file="gmfi.flowmfi"/>
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41 </test>
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42 </tests>
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43 <help><![CDATA[
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44 This tool generates the Mean, Median or Geometric Mean Fluorescence Intensity of a FLOCK output file.
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45
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46 -----
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47
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48 **Input file**
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49
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50 This tool reads in a FLOCK output file.
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51
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52 **Output file**
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53
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54 The output is a table containing the mean, median or geometric mean fluorescent intensity values of each marker within each population defined by FLOCK.
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55
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56 -----
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57
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58 **Example**
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59
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60 *Input*::
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61
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62 Marker1 Marker2 Marker3 Population
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63 34 45 12 1
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64 13 65 10 5
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65 19 62 98 2
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66 32 46 10 1
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67
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68 *Output*::
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69
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70 Population Marker1 Marker2 Marker3
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71 1 38 49 10
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72 2 21 63 100
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73 3 31 52 45
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74 4 11 78 25
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75 ]]>
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76 </help>
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77 </tool>
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