Mercurial > repos > immport-devteam > fcs_summary
comparison fcs_summary/FCSstats.xml @ 0:1d926a8daa92 draft
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author | immport-devteam |
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date | Mon, 27 Feb 2017 12:53:11 -0500 |
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-1:000000000000 | 0:1d926a8daa92 |
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1 <tool id="get_fcs_stats" name="Get summary" version="1.0"> | |
2 <description>of FCS files.</description> | |
3 <requirements> | |
4 <requirement type="package" version="3.3.0">r</requirement> | |
5 <requirement type="package" version="1.38.2">bioconductor-flowcore</requirement> | |
6 </requirements> | |
7 <stdio> | |
8 <exit_code range="2:" level="fatal" description="See stderr for more details." /> | |
9 </stdio> | |
10 <command><![CDATA[ | |
11 Rscript --slave --vanilla $__tool_directory__/FCSstats.R --args "${input}" "${output}" | |
12 ]]> | |
13 </command> | |
14 <inputs> | |
15 <param format="fcs" name="input" type="data" label="FCS file"/> | |
16 </inputs> | |
17 <outputs> | |
18 <data format="txt" name="output" label="Summary statisitics of ${input.name}"/> | |
19 </outputs> | |
20 <tests> | |
21 <test> | |
22 <param name="input" value="testfcs1.fcs"/> | |
23 <output name="output" file="summary.txt"/> | |
24 </test> | |
25 </tests> | |
26 <help><![CDATA[ | |
27 This tool generates a summary of a FCS file and list of markers. | |
28 | |
29 ----- | |
30 | |
31 **Input file** | |
32 | |
33 This tool uses valid FCS files as input. | |
34 | |
35 **Output file** | |
36 | |
37 FCS file summary includes number of events, list of markers and parameters, and summary statistics for each. | |
38 | |
39 ----- | |
40 | |
41 **Example** | |
42 | |
43 *Output*:: | |
44 | |
45 events parameters | |
46 20000 6 | |
47 | |
48 | |
49 ========================= | |
50 == FCS SUMMARY == | |
51 ========================= | |
52 FSC-H SSC-H FL1-H FL2-H FL3-H FL4-H | |
53 Min. 261 23 0.0 0.0 0.0 0.0 | |
54 1st Qu. 371 120 129.0 153.0 257.0 252.0 | |
55 Median 432 196 206.0 237.0 432.0 331.0 | |
56 Mean 512 476 284.8 236.7 433.2 372.3 | |
57 3rd Qu. 657 1023 499.0 297.0 628.0 510.0 | |
58 Max. 1023 1023 729.0 925.0 1023.0 1023.0 | |
59 | |
60 | |
61 ========================= | |
62 == MARKERS IN FCS == | |
63 ========================= | |
64 channels markers | |
65 1 FSC-H Forward Scatter | |
66 2 SSC-H Side Scatter | |
67 3 FL1-H FITC CD4 | |
68 4 FL2-H PE CD25 | |
69 5 FL3-H PP CD3 | |
70 6 FL4-H APC CD45RA | |
71 ]]> | |
72 </help> | |
73 </tool> |