Mercurial > repos > immport-devteam > generate_mfi

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
author azomics
date Wed, 22 Jul 2020 15:41:56 -0400
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91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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1 <tool id="generate_mfi" name="Generate the centroids" version="1.0+galaxy0" profile="18.01">
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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2 <description>from a flow result file</description>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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3 <requirements>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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4 <requirement type="package" version="1.0.5">pandas</requirement>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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5 <requirement type="package" version="1.5.1">scipy</requirement>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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6 </requirements>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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7 <stdio>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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8 <exit_code range="1:" />
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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9 </stdio>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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10 <command><![CDATA[
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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11 python '$__tool_directory__/generateMFI.py' -i '${input}' -o '${output}' -M '${mfi}'
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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12 ]]>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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13 </command>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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14 <inputs>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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15 <param format="flowclr" name="input" type="data" label="Flow Text file"/>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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16 <param name="mfi" type="select" label="Calculate centroids using:">
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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17 <option value="mfi" selected="true">Mean Fluorescence Intensity</option>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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18 <option value="mdfi">Median Fluorescence Intensity</option>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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19 <option value="gmfi">Geometric Mean Fluorescence Intensity</option>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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20 </param>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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21 </inputs>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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22 <outputs>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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23 <data format="flowmfi" name="output" label="${mfi} centroids from ${input.name}"/>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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24 </outputs>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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25 <tests>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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26 <test>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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27 <param name="input" value="input.flowclr"/>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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28 <param name="mfi" value="mfi"/>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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29 <output name="output" file="mfi.flowmfi"/>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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30 </test>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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31 <test>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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32 <param name="input" value="input.flowclr"/>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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33 <param name="mfi" value="mdfi"/>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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34 <output name="output" file="mdfi.flowmfi"/>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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35 </test>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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36 <test>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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37 <param name="input" value="input.flowclr"/>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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38 <param name="mfi" value="gmfi"/>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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39 <output name="output" file="gmfi.flowmfi"/>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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40 </test>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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41 </tests>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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42 <help><![CDATA[
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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43 This tool generates the Mean, Median or Geometric Mean Fluorescence Intensity of clustered flow files.
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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44 .. class:: infomark
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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45 Tip: This tool can be used to generate the centroids table required by the visualization tool multiple samples mapping result.
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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46 -----
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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47 **Input file**
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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48 This tool reads in a tab-separated file containing markers fluorescence intensities for each event as well as population or cluster attribution, for instance text output from a FLOCK or FlowSOM run.
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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49 **Output file**
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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50 The output is a table containing the mean, median or geometric mean fluorescent intensity values of each marker within each population or cluster defined in the input file.
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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51 -----
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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52 **Example**
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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53 *Input*::
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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54 Marker1 Marker2 Marker3 ... Population
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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55 34 45 12 ... 1
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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56 13 65 10 ... 5
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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57 19 62 98 ... 2
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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58 32 46 10 ... 1
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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59 ... ... ... ... ...
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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60 *Output*::
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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61 Population Marker1 Marker2 Marker3 ...
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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62 1 38 49 10 ...
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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63 2 21 63 100 ...
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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64 3 31 52 45 ...
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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65 4 11 78 25 ...
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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66 ... ... ... ... ...
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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67 ]]>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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68 </help>
91e856e5ec7a "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/generate_mfi commit a1f464ea7fe4a5d1b71664ef924544010036522a"
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69 </tool>