Mercurial > repos > immport-devteam > extract_fcs_keywords
comparison extract_fcs_keywords/extractKeywords.xml @ 0:dc00746654dc draft
Uploaded
author | immport-devteam |
---|---|
date | Mon, 27 Feb 2017 12:49:02 -0500 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:dc00746654dc |
---|---|
1 <tool id="extract_fcs_keywords" name="Extract keywords" version="1.0"> | |
2 <description>from 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="1:" /> | |
9 </stdio> | |
10 <command><![CDATA[ | |
11 Rscript --slave --vanilla $__tool_directory__/FCSKeyword.R --args "${input}" "${keyword_file}" | |
12 ]]> | |
13 </command> | |
14 <inputs> | |
15 <param format="fcs" name="input" type="data" label="FCS file"/> | |
16 </inputs> | |
17 <outputs> | |
18 <data format="tabular" name="keyword_file" label="Extract Keywords on ${input.name}"/> | |
19 </outputs> | |
20 <tests> | |
21 <test> | |
22 <param name="input" value="testfcs1.fcs"/> | |
23 <output name="keyword_file" file="out.tabular" lines_diff="2"/> | |
24 </test> | |
25 </tests> | |
26 <help><![CDATA[ | |
27 This tool extracts the Keywords from a FCS file. | |
28 | |
29 ----- | |
30 | |
31 **Input files** | |
32 | |
33 This tool uses FCS files as input. | |
34 | |
35 **Output file** | |
36 | |
37 The list of FCS file headers is output. | |
38 | |
39 ----- | |
40 | |
41 **Example** | |
42 | |
43 FCSversion=2 | |
44 | |
45 $BYTEORD=4,3,2,1 | |
46 | |
47 $DATATYPE=I | |
48 | |
49 $NEXTDATA=0 | |
50 | |
51 $SYS=Macintosh System Software 9.2.2 | |
52 | |
53 CREATOR=CELLQuest 3.3 | |
54 | |
55 $TOT=20000 | |
56 | |
57 $MODE=L | |
58 | |
59 $PAR=6 | |
60 | |
61 $P1N=FSC-H | |
62 | |
63 . | |
64 | |
65 .. | |
66 | |
67 ... | |
68 ]]> | |
69 </help> | |
70 </tool> |