annotate snpsplit.xml @ 6:e711f63e99ff draft

Uploaded
author rreumerman
date Fri, 05 Apr 2013 05:06:42 -0400
parents bd5692103d5b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
1 <tool id="snpsplit" name="SNP splitter">
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
2
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
3 <description>splits multicharacter entries into separate lines</description>
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
4
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
5 <command interpreter="python">snpsplit.py $input $output</command>
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
6
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
7 <inputs>
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
8
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
9 <param name="input" type="data" format="tabular" label="SNP table" />
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
10
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
11 </inputs>
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
12
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
13 <outputs>
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
14
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
15 <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
16
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
17 </outputs>
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
18
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
19 <help>
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
20
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
21
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
22 **What it does**
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
23
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
24
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
25
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
26 SNPsplit prepares tab-delimited SNP files for TRAMS. It checks each line for entries that contain multiple consecutive bases and splits them over several lines.
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
27
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
28
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
29
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
30 - **Input**: tab delimited, format: Position Ref Pol
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
31 - Position is 1-based genomic coordinate
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
32
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
33 - Ref is the reference sequence
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
34
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
35 - Pol is the polymorphism sequence
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
36
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
37
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
38
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
39 Ref en Mut sequences consisting of more than one character will be split up into separate lines. Example:
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
40
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
41
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
42
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
43 **Input**:
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
44
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
45
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
46 === === ===
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
47
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
48 123 CGT ATG
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
49
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
50 === === ===
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
51
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
52
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
53
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
54 **Output**:
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
55
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
56
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
57 === = =
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
58
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
59 123 C A
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
60
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
61 124 G T
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
62
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
63 125 T G
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
64
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
65 === = =
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
66
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
67
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
68
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
69 Bases that are the same in both columns, will be skipped. Example:
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
70
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
71
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
72
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
73 **Input**:
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
74
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
75
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
76 === ===== ===
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
77
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
78 123 C*G*T AGG
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
79
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
80 === ===== ===
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
81
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
82
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
83
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
84 **Output**:
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
85
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
86
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
87 === = =
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
88
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
89 123 C A
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
90
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
91 125 T G
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
92
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
93 === = =
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
94
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
95
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
96 </help>
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
97
bd5692103d5b Uploaded
rreumerman
parents:
diff changeset
98 </tool>