annotate microsatcompat.xml @ 14:20dc70f85ff7 draft default tip

Uploaded
author arkarachai-fungtammasan
date Sun, 24 Jul 2016 18:15:32 -0400
parents d5ed5c2e25c3
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
d5ed5c2e25c3 Uploaded
arkarachai-fungtammasan
parents: 0
diff changeset
1 <tool id="microsatcompat" name="Check STR motif compatibility between reference and read STRs" version="1.0.0">
0
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
2 <description> </description>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
3 <command interpreter="python">microsatcompat.py $input $column1 $column2 > $output </command>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
4
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
5 <inputs>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
6 <param name="input" type="data" label="Select input" />
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
7 <param name="column1" type="integer" value="4" label="First column number" />
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
8 <param name="column2" type="integer" value="10" label="Second column number" />
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
9 </inputs>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
10 <outputs>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
11 <data format="tabular" name="output" />
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
12
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
13 </outputs>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
14 <tests>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
15 <!-- Test data with valid values -->
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
16 <test>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
17 <param name="input" value="microsatcompat_in.txt"/>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
18 <param name="column1" value="4"/>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
19 <param name="column2" value="10"/>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
20 <output name="output" file="microsatcompat_out.txt"/>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
21 </test>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
22
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
23 </tests>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
24 <help>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
25
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
26
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
27 .. class:: infomark
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
28
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
29 **What it does**
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
30
2
d5ed5c2e25c3 Uploaded
arkarachai-fungtammasan
parents: 0
diff changeset
31 This tool is used to select only those input lines that have compatible STR motifs between the two user-specified columns. Two STR motifs are called compatible if they are either identical, or complementary, or produce the same sequence on rotating the start of the motif. For example, **A** is considered compatible with **A** and its reverse complement **T**. Similarly, **AGG** considered compatible with **AGG**, its reverse complement **TCC**, and their rotations **GGA**, **GAG**, **CCT** and **CTC**.
0
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
32
2
d5ed5c2e25c3 Uploaded
arkarachai-fungtammasan
parents: 0
diff changeset
33 For STR-FM pipeline (profiling STRs in short read data), this tool can be used to make sure that the STRs in the reads have the compatible motif as the STRs in the reference at the corresponding mapped location.
0
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
34
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
35 **Citation**
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
36
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
37 When you use this tool, please cite **Fungtammasan A, Ananda G, Hile SE, Su MS, Sun C, Harris R, Medvedev P, Eckert K, Makova KD. 2015. Accurate Typing of Short Tandem Repeats from Genome-wide Sequencing Data and its Applications, Genome Research**
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
38
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
39 **Input**
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
40
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
41 The input files can be any tab delimited file.
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
42
2
d5ed5c2e25c3 Uploaded
arkarachai-fungtammasan
parents: 0
diff changeset
43 If this tool is used in STR-FM pipeline for STRs profiling, it should contains:
0
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
44
2
d5ed5c2e25c3 Uploaded
arkarachai-fungtammasan
parents: 0
diff changeset
45 - Column 1 = STR location in reference chromosome
d5ed5c2e25c3 Uploaded
arkarachai-fungtammasan
parents: 0
diff changeset
46 - Column 2 = STR location in reference start
d5ed5c2e25c3 Uploaded
arkarachai-fungtammasan
parents: 0
diff changeset
47 - Column 3 = STR location in reference stop
d5ed5c2e25c3 Uploaded
arkarachai-fungtammasan
parents: 0
diff changeset
48 - Column 4 = STR location in reference motif
d5ed5c2e25c3 Uploaded
arkarachai-fungtammasan
parents: 0
diff changeset
49 - Column 5 = STR location in reference length
d5ed5c2e25c3 Uploaded
arkarachai-fungtammasan
parents: 0
diff changeset
50 - Column 6 = STR location in reference motif size
d5ed5c2e25c3 Uploaded
arkarachai-fungtammasan
parents: 0
diff changeset
51 - Column 7 = length of STR (bp)
d5ed5c2e25c3 Uploaded
arkarachai-fungtammasan
parents: 0
diff changeset
52 - Column 8 = length of left flanking region (bp)
d5ed5c2e25c3 Uploaded
arkarachai-fungtammasan
parents: 0
diff changeset
53 - Column 9 = length of right flanking region (bp)
0
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
54 - Column 10 = repeat motif (bp)
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
55 - Column 11 = hamming distance
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
56 - Column 12 = read name
2
d5ed5c2e25c3 Uploaded
arkarachai-fungtammasan
parents: 0
diff changeset
57 - Column 13 = read sequence with soft masking of STR
0
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
58 - Column 14 = read quality (the same Phred score scale as input)
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
59 - Column 15 = read name (The same as column 12)
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
60 - Column 16 = chromosome
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
61 - Column 17 = left flanking region start
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
62 - Column 18 = left flanking region stop
2
d5ed5c2e25c3 Uploaded
arkarachai-fungtammasan
parents: 0
diff changeset
63 - Column 19 = STR start as infer from pair-end
d5ed5c2e25c3 Uploaded
arkarachai-fungtammasan
parents: 0
diff changeset
64 - Column 20 = STR stop as infer from pair-end
0
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
65 - Column 21 = right flanking region start
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
66 - Column 22 = right flanking region stop
2
d5ed5c2e25c3 Uploaded
arkarachai-fungtammasan
parents: 0
diff changeset
67 - Column 23 = STR length in reference
d5ed5c2e25c3 Uploaded
arkarachai-fungtammasan
parents: 0
diff changeset
68 - Column 24 = STR sequence in reference
0
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
69
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
70 **Output**
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
71
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
72 The same as input format.
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
73
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
74
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
75 </help>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
76 </tool>