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comparison FCSstats.xml @ 1:d2749aa59d20 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_summary commit 72efaa6d006ddda6c8eed10ec9ba541cbdecf3a8"
author azomics
date Mon, 22 Jun 2020 17:33:38 -0400
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0:1d926a8daa92 1:d2749aa59d20
1 <tool id="get_fcs_stats" name="Get summary" version="1.0+galaxy0">
2 <description>of FCS files</description>
3 <requirements>
4 <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="2:" level="fatal" description="See stderr for more details." />
8 </stdio>
9 <command><![CDATA[
10 Rscript --slave --vanilla '$__tool_directory__/FCSstats.R' '${input}' '${output}'
11 ]]>
12 </command>
13 <inputs>
14 <param format="fcs" name="input" type="data" label="FCS file"/>
15 </inputs>
16 <outputs>
17 <data format="txt" name="output" label="Summary statisitics of ${input.name}"/>
18 </outputs>
19 <tests>
20 <test>
21 <param name="input" value="testfcs1.fcs"/>
22 <output name="output" file="summary.txt" compare="sim_size"/>
23 </test>
24 </tests>
25 <help><![CDATA[
26 This tool generates a summary of a FCS file and list of markers.
27
28 -----
29
30 **Input file**
31
32 This tool uses valid FCS files as input.
33
34 **Output file**
35
36 FCS file summary includes number of events, list of markers and parameters, and summary statistics for each.
37
38 -----
39
40 **Example**
41
42 *Output*::
43
44 events parameters
45 20000 6
46
47
48 =========================
49 == FCS SUMMARY ==
50 =========================
51 FSC-H SSC-H FL1-H FL2-H FL3-H FL4-H
52 Min. 261 23 0.0 0.0 0.0 0.0
53 1st Qu. 371 120 129.0 153.0 257.0 252.0
54 Median 432 196 206.0 237.0 432.0 331.0
55 Mean 512 476 284.8 236.7 433.2 372.3
56 3rd Qu. 657 1023 499.0 297.0 628.0 510.0
57 Max. 1023 1023 729.0 925.0 1023.0 1023.0
58
59
60 =========================
61 == MARKERS IN FCS ==
62 =========================
63 channels markers
64 1 FSC-H Forward Scatter
65 2 SSC-H Side Scatter
66 3 FL1-H FITC CD4
67 4 FL2-H PE CD25
68 5 FL3-H PP CD3
69 6 FL4-H APC CD45RA
70 ]]>
71 </help>
72 </tool>