Mercurial > repos > immport-devteam > fcs_summary
comparison fcs_summary/FCSstats.xml @ 0:1d926a8daa92 draft
Uploaded
| author | immport-devteam |
|---|---|
| date | Mon, 27 Feb 2017 12:53:11 -0500 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:1d926a8daa92 |
|---|---|
| 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> |