Mercurial > repos > immport-devteam > generate_mfi
comparison 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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-1:000000000000 | 0:2f6dcda6e74e |
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1 <tool id="generate_mfi" name="Generate the centroids" version="1.0"> | |
2 <description>from a flow result file</description> | |
3 <requirements> | |
4 <requirement type="package" version="0.17.1">pandas</requirement> | |
5 <requirement type="package" version="1.10.2">numpy</requirement> | |
6 <requirement type="package" version="0.16.0">scipy</requirement> | |
7 </requirements> | |
8 <stdio> | |
9 <exit_code range="1:" /> | |
10 </stdio> | |
11 <command><![CDATA[ | |
12 python $__tool_directory__/generateMFI.py -i "${input}" -o "${output}" -M "${mfi}" | |
13 ]]> | |
14 </command> | |
15 <inputs> | |
16 <param format="flowclr" name="input" type="data" label="Flow Text file"/> | |
17 <param name="mfi" type="select" label="Calculate centroids using:"> | |
18 <option value="mfi" selected="true">Mean Fluorescence Intensity</option> | |
19 <option value="mdfi">Median Fluorescence Intensity</option> | |
20 <option value="gmfi">Geometric Mean Fluorescence Intensity</option> | |
21 </param> | |
22 </inputs> | |
23 <outputs> | |
24 <data format="flowmfi" name="output" label="${mfi} centroids from ${input.name}"/> | |
25 </outputs> | |
26 <tests> | |
27 <test> | |
28 <param name="input" value="input.flowclr"/> | |
29 <param name="mfi" value="mfi"/> | |
30 <output name="output" file="mfi.flowmfi"/> | |
31 </test> | |
32 <test> | |
33 <param name="input" value="input.flowclr"/> | |
34 <param name="mfi" value="mdfi"/> | |
35 <output name="output" file="mdfi.flowmfi"/> | |
36 </test> | |
37 <test> | |
38 <param name="input" value="input.flowclr"/> | |
39 <param name="mfi" value="gmfi"/> | |
40 <output name="output" file="gmfi.flowmfi"/> | |
41 </test> | |
42 </tests> | |
43 <help><![CDATA[ | |
44 This tool generates the Mean, Median or Geometric Mean Fluorescence Intensity of a FLOCK output file. | |
45 | |
46 ----- | |
47 | |
48 **Input file** | |
49 | |
50 This tool reads in a FLOCK output file. | |
51 | |
52 **Output file** | |
53 | |
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. | |
55 | |
56 ----- | |
57 | |
58 **Example** | |
59 | |
60 *Input*:: | |
61 | |
62 Marker1 Marker2 Marker3 Population | |
63 34 45 12 1 | |
64 13 65 10 5 | |
65 19 62 98 2 | |
66 32 46 10 1 | |
67 | |
68 *Output*:: | |
69 | |
70 Population Marker1 Marker2 Marker3 | |
71 1 38 49 10 | |
72 2 21 63 100 | |
73 3 31 52 45 | |
74 4 11 78 25 | |
75 ]]> | |
76 </help> | |
77 </tool> |