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comparison generate_mfi/generateMFI.xml @ 0:2f6dcda6e74e draft

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author immport-devteam
date Mon, 27 Feb 2017 13:00:34 -0500
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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>