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