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/tools/fastx_toolkit/fastx_barcode_splitter.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 76 lines | 51 code | 23 blank | 2 comment | 0 complexity | 7fb0c68cb722818be2cc80376181f06d MD5 | raw file
 1<tool id="cshl_fastx_barcode_splitter" name="Barcode Splitter">
 2	<description></description>
 3	<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
 4	<command interpreter="bash">fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > $output </command>
 5
 6	<inputs>
 7		<param format="txt" name="BARCODE" type="data" label="Barcodes to use" />
 8		<param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" />
 9
10		<param name="EOL" type="select" label="Barcodes found at">
11			<option value="--bol">Start of sequence (5' end)</option>
12			<option value="--eol">End of sequence (3' end)</option>
13		</param>
14
15		<param name="mismatches" type="integer" size="3" value="2" label="Number of allowed mismatches" />
16		
17		<param name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" />
18	
19	</inputs>
20	
21	<tests>
22		<test>
23			<!-- Split a FASTQ file -->
24			<param name="BARCODE" value="fastx_barcode_splitter1.txt" />
25			<param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
26			<param name="EOL" value="Start of sequence (5' end)" />
27			<param name="mismatches" value="2" />
28			<param name="partial" value="0" />
29			<output name="output" file="fastx_barcode_splitter1.out" />
30		</test>
31	</tests>
32
33	<outputs>
34		<data format="html" name="output" />
35	</outputs>
36<help>
37
38**What it does**
39
40This tool splits a Solexa library (FASTQ file) or a regular FASTA file into several files, using barcodes as the split criteria.
41
42--------
43
44**Barcode file Format**
45
46Barcode files are simple text files.
47Each line should contain an identifier (descriptive name for the barcode), and the barcode itself (A/C/G/T), separated by a TAB character.
48Example::
49
50    #This line is a comment (starts with a 'number' sign)
51    BC1	GATCT
52    BC2	ATCGT
53    BC3	GTGAT
54    BC4 TGTCT
55    
56For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name).
57Sequences matching the barcode will be stored in the appropriate file.
58
59One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored.
60
61The output of this tool is an HTML file, displaying the split counts and the file locations.
62
63**Output Example**
64
65.. image:: ./static/fastx_icons/barcode_splitter_output_example.png
66
67
68------
69
70This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
71
72 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
73 
74</help>
75</tool>
76<!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->