Mercurial > repos > xuebing > sharplabtool
comparison tools/fastx_toolkit/fastx_barcode_splitter.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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-1:000000000000 | 0:9071e359b9a3 |
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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 | |
40 This 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 | |
46 Barcode files are simple text files. | |
47 Each line should contain an identifier (descriptive name for the barcode), and the barcode itself (A/C/G/T), separated by a TAB character. | |
48 Example:: | |
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 | |
56 For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name). | |
57 Sequences matching the barcode will be stored in the appropriate file. | |
58 | |
59 One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored. | |
60 | |
61 The 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 </help> | |
68 </tool> | |
69 <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> |