Mercurial > repos > immport-devteam > convert_fcs_to_text
comparison convert_fcs_to_text/convertFCSToText.xml @ 0:8e10184368a0 draft
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author | immport-devteam |
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date | Mon, 27 Feb 2017 12:45:51 -0500 |
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-1:000000000000 | 0:8e10184368a0 |
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1 <tool id="convert_fcs_to_text" name="Convert FCS to Text" version="1.0"> | |
2 <description>with no transformation.</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="1:" /> | |
9 </stdio> | |
10 <command><![CDATA[ | |
11 Rscript --slave --vanilla $__tool_directory__/FCSConvert.R --args "${input}" "${output_file}" $compensate | |
12 ]]> | |
13 </command> | |
14 <inputs> | |
15 <param format="fcs" name="input" type="data" label="FCS file"/> | |
16 <param name="compensate" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Compensate?"> | |
17 </param> | |
18 </inputs> | |
19 <outputs> | |
20 <data format="flowtext" name="output_file" label="No Transformation ${input.name}"/> | |
21 </outputs> | |
22 <tests> | |
23 <test> | |
24 <param name="input" value="testfcs1.fcs"/> | |
25 <param name="compensate" value="FALSE"/> | |
26 <output name="output_file" file="nocomp.flowtext"/> | |
27 </test> | |
28 <test> | |
29 <param name="input" value="testfcs1.fcs"/> | |
30 <param name="compensate" value="TRUE"/> | |
31 <output name="output_file" file="withcomp.flowtext"/> | |
32 </test> | |
33 </tests> | |
34 <help><![CDATA[ | |
35 This tool converts FCS files to text format with no tranformation. | |
36 | |
37 ----- | |
38 | |
39 **Input files** | |
40 | |
41 This tool requires valid FCS files as input. Files are processed serially. Applying compensation is an option for FCS files including a compensation matrix. | |
42 | |
43 **Output file** | |
44 | |
45 The output is tab-separated text, containing the fluorescence intensity values for each marker. | |
46 | |
47 ----- | |
48 | |
49 **Example**:: | |
50 | |
51 Forward Scatter Side Scatter Marker1 Marker2 Marker3 Marker4 | |
52 449 157 551 129 169 292 | |
53 894 1023 199 277 320 227 | |
54 262 73 437 69 0 146 | |
55 340 115 509 268 0 74 | |
56 ]]> | |
57 </help> | |
58 </tool> |