Mercurial > repos > immport-devteam > generate_mfi
diff generate_mfi/generateMFI.xml @ 0:2f6dcda6e74e draft
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author | immport-devteam |
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date | Mon, 27 Feb 2017 13:00:34 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generate_mfi/generateMFI.xml Mon Feb 27 13:00:34 2017 -0500 @@ -0,0 +1,77 @@ +<tool id="generate_mfi" name="Generate the centroids" version="1.0"> + <description>from a flow result file</description> + <requirements> + <requirement type="package" version="0.17.1">pandas</requirement> + <requirement type="package" version="1.10.2">numpy</requirement> + <requirement type="package" version="0.16.0">scipy</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + python $__tool_directory__/generateMFI.py -i "${input}" -o "${output}" -M "${mfi}" + ]]> + </command> + <inputs> + <param format="flowclr" name="input" type="data" label="Flow Text file"/> + <param name="mfi" type="select" label="Calculate centroids using:"> + <option value="mfi" selected="true">Mean Fluorescence Intensity</option> + <option value="mdfi">Median Fluorescence Intensity</option> + <option value="gmfi">Geometric Mean Fluorescence Intensity</option> + </param> + </inputs> + <outputs> + <data format="flowmfi" name="output" label="${mfi} centroids from ${input.name}"/> + </outputs> + <tests> + <test> + <param name="input" value="input.flowclr"/> + <param name="mfi" value="mfi"/> + <output name="output" file="mfi.flowmfi"/> + </test> + <test> + <param name="input" value="input.flowclr"/> + <param name="mfi" value="mdfi"/> + <output name="output" file="mdfi.flowmfi"/> + </test> + <test> + <param name="input" value="input.flowclr"/> + <param name="mfi" value="gmfi"/> + <output name="output" file="gmfi.flowmfi"/> + </test> + </tests> + <help><![CDATA[ + This tool generates the Mean, Median or Geometric Mean Fluorescence Intensity of a FLOCK output file. + +----- + +**Input file** + +This tool reads in a FLOCK output file. + +**Output file** + +The output is a table containing the mean, median or geometric mean fluorescent intensity values of each marker within each population defined by FLOCK. + +----- + +**Example** + +*Input*:: + + Marker1 Marker2 Marker3 Population + 34 45 12 1 + 13 65 10 5 + 19 62 98 2 + 32 46 10 1 + +*Output*:: + + Population Marker1 Marker2 Marker3 + 1 38 49 10 + 2 21 63 100 + 3 31 52 45 + 4 11 78 25 + ]]> + </help> +</tool>