Mercurial > repos > arkarachai-fungtammasan > str_fm

comparison space2underscore_readname.xml @ 2:d5ed5c2e25c3 draft

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author arkarachai-fungtammasan
date Wed, 22 Apr 2015 12:48:40 -0400
parents 07588b899c13
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1:f2bab38e3cbd 2:d5ed5c2e25c3
1 <tool id="space2underscore_readname" name="Read name modifier" version="1.0.0"> 1 <tool id="space2underscore_readname" name="Read name modifier" version="1.0.0">
2 <description>--change space to underscore of a specific column</description> 2 <description>--change space to underscore in the read name column</description>
3 <command interpreter="python">changespacetounderscore_readname.py $input $output $column_n </command> 3 <command interpreter="python">changespacetounderscore_readname.py $input $output $column_n </command>
4 4
5 <inputs> 5 <inputs>
6 <param name="input" type="data" label="Select input" /> 6 <param name="input" type="data" label="Select input" />
7 <param name="column_n" type="integer" value="6" label="Select column to modify" /> 7 <param name="column_n" type="integer" value="6" label="Select column to modify" />
24 24
25 .. class:: infomark 25 .. class:: infomark
26 26
27 **What it does** 27 **What it does**
28 28
29 This tool is used to change space to underscore. For TRFM pipeline (profiling microsatellites in short read data), this tool is used to change space in read name to underscore to prevent the downstream tools which might recognize incorrect column number due to space in read name. If the input do not have space in read name, this step can be skipped. 29 The readname produced by the "STR detection" step may contain spaces instead of underscores, which will cause downstream tools that use space as a column delimiter to fail. This tool will help convert space to underscore.
30 If your input does not have spaces in readname column, this step can be skipped.
30 31
31 **Citation** 32 **Citation**
32 33
33 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** 34 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**
34 35
35 **Input** 36 **Input**
36 37
37 The input files can be any tab delimited file. 38 The input files can be any tab delimited file.
38 39
39 If this tool is used in TRFM microsatellite profiling, it should be in the same format as output from **microsatellite detection program**. This format contains **length of repeat**, **length of left flanking region**, **length of right flanking region**, **repeat motif**, **hamming (editing) distance**, **read name**, **read sequence**, **read quality score** 40 If this tool is used in STR-FM for STRs profiling, it should be in the same format as output from **STR detection program**. This format contains **length of repeat**, **length of left flanking region**, **length of right flanking region**, **repeat motif**, **hamming (editing) distance**, **read name**, **read sequence**, **read quality score**
40 41
41 **Output** 42 **Output**
42 43
43 The same as input format. 44 The same as input format.
44 45