|
0
|
1 <tool id="cga_junctiondiff" name="junctiondiff(beta)" version="0.0.1">
|
|
|
2
|
|
|
3 <description>reports difference between junction calls</description> <!--adds description in toolbar-->
|
|
|
4
|
|
|
5 <requirements>
|
|
|
6 <requirement type="binary">cgatools</requirement>
|
|
|
7 </requirements>
|
|
|
8
|
|
|
9 <command> <!--run executable-->
|
|
|
10 cgatools junctiondiff --beta -h
|
|
|
11 </command>
|
|
|
12
|
|
|
13 <outputs>
|
|
|
14 <data format="tabular" name="output" />
|
|
|
15 </outputs>
|
|
|
16
|
|
|
17 <inputs>
|
|
|
18 </inputs>
|
|
|
19
|
|
|
20 <help>
|
|
|
21
|
|
|
22 **What it does**
|
|
|
23
|
|
|
24 This tool reports difference between junction calls of Complete Genomics junctions files
|
|
|
25
|
|
|
26 cgatools: http://sourceforge.net/projects/cgatools/files/
|
|
|
27
|
|
|
28 -----
|
|
|
29
|
|
|
30 **cgatools Manual**::
|
|
|
31
|
|
|
32 COMMAND NAME
|
|
|
33 junctiondiff - Reports difference between junction calls of Complete Genomics junctions files.
|
|
|
34
|
|
|
35 DESCRIPTION
|
|
|
36 junctiondiff takes two junction files A and B as input and produces the
|
|
|
37 following output:
|
|
|
38 - "diff-inputFileName" - the junctions from an input file A that are not
|
|
|
39 present in input file B.
|
|
|
40 - "report.txt" - a brief summary report (if --statout is used)
|
|
|
41
|
|
|
42 Two junctions are considered equivalent if:
|
|
|
43 - they come from different files
|
|
|
44 - left and right positions of one junction are not more than "--distance"
|
|
|
45 bases apart from the corresponding positions of another junction
|
|
|
46 - the junction scores are equal or above the scoreThreshold
|
|
|
47 - they are on the same strands
|
|
|
48
|
|
|
49 OPTIONS
|
|
|
50 -h [ --help ]
|
|
|
51 Print this help message.
|
|
|
52
|
|
|
53 --beta
|
|
|
54 This is a beta command. To run this command, you must pass the --beta
|
|
|
55 flag.
|
|
|
56
|
|
|
57 -s [ --reference ] arg
|
|
|
58 Reference file.
|
|
|
59
|
|
|
60 -a [ --junctionsA ] arg
|
|
|
61 input junction file A.
|
|
|
62
|
|
|
63 -b [ --junctionsB ] arg
|
|
|
64 input junction file B.
|
|
|
65
|
|
|
66 -A [ --scoreThresholdA ] arg (=10)
|
|
|
67 score threshold value for the input file A.
|
|
|
68
|
|
|
69 -B [ --scoreThresholdB ] arg (=0)
|
|
|
70 score threshold value for the input file B.
|
|
|
71
|
|
|
72 -d [ --distance ] arg (=200)
|
|
|
73 Max distance between coordinates of potentially compatible junctions.
|
|
|
74
|
|
|
75 -l [ --minlength ] arg (=500)
|
|
|
76 Minimum deletion junction length to be included into the difference
|
|
|
77 file.
|
|
|
78
|
|
|
79 -o [ --output-prefix ] arg
|
|
|
80 The path prefix for all the output reports.
|
|
|
81
|
|
|
82 -S [ --statout ]
|
|
|
83 (Debug) Report various input file statistics. Experimental feature.
|
|
|
84
|
|
|
85 SUPPORTED FORMAT_VERSION
|
|
|
86 1.5 or later
|
|
|
87 </help>
|
|
|
88 </tool>
|
