Mercurial > repos > devteam > fastx_barcode_splitter
annotate fastx_barcode_splitter.xml @ 1:7b5eb2503f6d
Remove spurious version strings.
| author | Dave Bouvier <dave@bx.psu.edu> |
|---|---|
| date | Tue, 26 Nov 2013 12:46:41 -0500 |
| parents | 6cbe88c680bb |
| children | 1a20fbb8bad8 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="cshl_fastx_barcode_splitter" version="1.0.0" name="Barcode Splitter"> |
| 2 <description></description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="bash">fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > $output </command> | |
| 7 | |
| 8 <inputs> | |
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7b5eb2503f6d
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
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9 <param format="txt" name="BARCODE" type="data" label="Barcodes to use" /> |
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7b5eb2503f6d
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
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10 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" /> |
| 0 | 11 |
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7b5eb2503f6d
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
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12 <param name="EOL" type="select" label="Barcodes found at"> |
| 0 | 13 <option value="--bol">Start of sequence (5' end)</option> |
| 14 <option value="--eol">End of sequence (3' end)</option> | |
| 15 </param> | |
| 16 | |
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1
7b5eb2503f6d
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
17 <param name="mismatches" type="integer" size="3" value="2" label="Number of allowed mismatches" /> |
| 0 | 18 |
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1
7b5eb2503f6d
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
19 <param name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" /> |
| 0 | 20 |
| 21 </inputs> | |
| 22 | |
| 23 <tests> | |
| 24 <test> | |
| 25 <!-- Split a FASTQ file --> | |
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1
7b5eb2503f6d
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
26 <param name="BARCODE" value="fastx_barcode_splitter1.txt" /> |
|
7b5eb2503f6d
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
27 <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" /> |
|
7b5eb2503f6d
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
28 <param name="EOL" value="Start of sequence (5' end)" /> |
|
7b5eb2503f6d
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
29 <param name="mismatches" value="2" /> |
|
7b5eb2503f6d
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
30 <param name="partial" value="0" /> |
|
7b5eb2503f6d
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
31 <output name="output" file="fastx_barcode_splitter1.out" /> |
| 0 | 32 </test> |
| 33 </tests> | |
| 34 | |
| 35 <outputs> | |
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1
7b5eb2503f6d
Remove spurious version strings.
Dave Bouvier <dave@bx.psu.edu>
parents:
0
diff
changeset
|
36 <data format="html" name="output" /> |
| 0 | 37 </outputs> |
| 38 <help> | |
| 39 | |
| 40 **What it does** | |
| 41 | |
| 42 This tool splits a Solexa library (FASTQ file) or a regular FASTA file into several files, using barcodes as the split criteria. | |
| 43 | |
| 44 -------- | |
| 45 | |
| 46 **Barcode file Format** | |
| 47 | |
| 48 Barcode files are simple text files. | |
| 49 Each line should contain an identifier (descriptive name for the barcode), and the barcode itself (A/C/G/T), separated by a TAB character. | |
| 50 Example:: | |
| 51 | |
| 52 #This line is a comment (starts with a 'number' sign) | |
| 53 BC1 GATCT | |
| 54 BC2 ATCGT | |
| 55 BC3 GTGAT | |
| 56 BC4 TGTCT | |
| 57 | |
| 58 For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name). | |
| 59 Sequences matching the barcode will be stored in the appropriate file. | |
| 60 | |
| 61 One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored. | |
| 62 | |
| 63 The output of this tool is an HTML file, displaying the split counts and the file locations. | |
| 64 | |
| 65 **Output Example** | |
| 66 | |
| 67 .. image:: ${static_path}/fastx_icons/barcode_splitter_output_example.png | |
| 68 | |
| 69 | |
| 70 ------ | |
| 71 | |
| 72 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. | |
| 73 | |
| 74 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ | |
| 75 | |
| 76 </help> | |
| 77 <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> | |
| 78 </tool> |