Mercurial > repos > immport-devteam > generate_mfi
comparison generateMFI.xml @ 1:91e856e5ec7a draft default tip
"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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| children |
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| 0:2f6dcda6e74e | 1:91e856e5ec7a |
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| 1 <tool id="generate_mfi" name="Generate the centroids" version="1.0+galaxy0" profile="18.01"> | |
| 2 <description>from a flow result file</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.0.5">pandas</requirement> | |
| 5 <requirement type="package" version="1.5.1">scipy</requirement> | |
| 6 </requirements> | |
| 7 <stdio> | |
| 8 <exit_code range="1:" /> | |
| 9 </stdio> | |
| 10 <command><![CDATA[ | |
| 11 python '$__tool_directory__/generateMFI.py' -i '${input}' -o '${output}' -M '${mfi}' | |
| 12 ]]> | |
| 13 </command> | |
| 14 <inputs> | |
| 15 <param format="flowclr" name="input" type="data" label="Flow Text file"/> | |
| 16 <param name="mfi" type="select" label="Calculate centroids using:"> | |
| 17 <option value="mfi" selected="true">Mean Fluorescence Intensity</option> | |
| 18 <option value="mdfi">Median Fluorescence Intensity</option> | |
| 19 <option value="gmfi">Geometric Mean Fluorescence Intensity</option> | |
| 20 </param> | |
| 21 </inputs> | |
| 22 <outputs> | |
| 23 <data format="flowmfi" name="output" label="${mfi} centroids from ${input.name}"/> | |
| 24 </outputs> | |
| 25 <tests> | |
| 26 <test> | |
| 27 <param name="input" value="input.flowclr"/> | |
| 28 <param name="mfi" value="mfi"/> | |
| 29 <output name="output" file="mfi.flowmfi"/> | |
| 30 </test> | |
| 31 <test> | |
| 32 <param name="input" value="input.flowclr"/> | |
| 33 <param name="mfi" value="mdfi"/> | |
| 34 <output name="output" file="mdfi.flowmfi"/> | |
| 35 </test> | |
| 36 <test> | |
| 37 <param name="input" value="input.flowclr"/> | |
| 38 <param name="mfi" value="gmfi"/> | |
| 39 <output name="output" file="gmfi.flowmfi"/> | |
| 40 </test> | |
| 41 </tests> | |
| 42 <help><![CDATA[ | |
| 43 This tool generates the Mean, Median or Geometric Mean Fluorescence Intensity of clustered flow files. | |
| 44 .. class:: infomark | |
| 45 Tip: This tool can be used to generate the centroids table required by the visualization tool multiple samples mapping result. | |
| 46 ----- | |
| 47 **Input file** | |
| 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. | |
| 49 **Output file** | |
| 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. | |
| 51 ----- | |
| 52 **Example** | |
| 53 *Input*:: | |
| 54 Marker1 Marker2 Marker3 ... Population | |
| 55 34 45 12 ... 1 | |
| 56 13 65 10 ... 5 | |
| 57 19 62 98 ... 2 | |
| 58 32 46 10 ... 1 | |
| 59 ... ... ... ... ... | |
| 60 *Output*:: | |
| 61 Population Marker1 Marker2 Marker3 ... | |
| 62 1 38 49 10 ... | |
| 63 2 21 63 100 ... | |
| 64 3 31 52 45 ... | |
| 65 4 11 78 25 ... | |
| 66 ... ... ... ... ... | |
| 67 ]]> | |
| 68 </help> | |
| 69 </tool> |