annotate PEsortedSAM2readprofile.xml @ 1:f2bab38e3cbd draft

Deleted selected files
author arkarachai-fungtammasan
date Wed, 01 Apr 2015 17:06:29 -0400
parents 07588b899c13
children d5ed5c2e25c3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
1 <tool id="PEsortedSAM2readprofile" name="Combine mapped flaked bases" version="1.0.0">
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
2 <description> from SAM file sorted by readname </description>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
3 <command interpreter="python2.7">PEsortedSAM2readprofile.py $flankedbasesSAM $twobitref $maxTRlength $maxoriginalreadlength $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="flankedbasesSAM" type="data" format="sam" label="Select sorted SAM file (by readname) of flaked bases" />
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
7 <param name="twobitref" type="data" label="Select twobit file reference genome" />
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
8 <param name="maxTRlength" type="integer" value="100" label="Maximum expected microsatellite length (bp)" />
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
9 <param name="maxoriginalreadlength" type="integer" value="101" label="Maxinum original read length" />
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
10
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
11 </inputs>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
12 <outputs>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
13 <data name="output" format="tabular" />
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
14 </outputs>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
15 <tests>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
16 <!-- Test data with valid values -->
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
17 <test>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
18 <param name="flankedbasesSAM" value="samplesortedPESAM_C.sam"/>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
19 <param name="twobitref" value="shifted.2bit"/>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
20 <param name="maxTRlength" value="100"/>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
21 <param name="maxoriginalreadlength" value="250"/>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
22 <output name="output" file="samplePESAM_2_profile_C.txt"/>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
23 </test>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
24
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
25 </tests>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
26 <help>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
27
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
28
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
29 .. class:: infomark
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
30
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
31 **What it does**
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
32
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
33 - This tool will take SAM file sorted by read name, remove unpaired reads, report microsatellites sequences in the reference genome that correspond to the space between paired end reads. Coordinate of start and stop for left and right flanking regions of microsatellites and microsatellite itself as inferred from paired end reads will also be reported.
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
34 - These microsatellites in reference can be used to filter out reads that do not contain microsatellites that concur with microsatellites in reference where the reads mapped to.
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
35
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
36 **Citation**
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
37
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
38 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
39
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
40 **Input**
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
41
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
42 - Sorted SAM files by read name
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
43
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
44 **Output**
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
45
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
46 The output will combined two lines of input which are paired. The output format is as follow.
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
47
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
48 - Column 1 = read name
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
49 - Column 2 = chromosome
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
50 - Column 3 = left flanking region start
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
51 - Column 4 = left flanking region stop
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
52 - Column 5 = microsatellite start
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
53 - Column 6 = microsatellite stop
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
54 - Column 7 = right flanking region start
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
55 - Column 8 = right flanking region stop
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
56 - Column 9 = microsatellite length in reference
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
57 - Column 10= microsatellite sequence in reference
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
58
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
59
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
60
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
61 </help>
07588b899c13 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
62 </tool>