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comparison fastx_barcode_splitter.xml @ 0:84bbf4fd24c3 draft

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Initial toolshed version with support for separate index reads and automatic loading of results into Galaxy history.
author lparsons
date Fri, 08 Nov 2013 09:53:39 -0500
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children b7b3d008e2d3
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-1:000000000000 0:84bbf4fd24c3
1 <tool id="cshl_princeton_fastx_barcode_splitter" version="1.1" name="Barcode Splitter" force_history_refresh="True">
2 <description></description>
3 <command interpreter="bash">
4 fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "primary_$output.id" "$__new_file_path__" $input.extension --mismatches $mismatches --partial $partial
5 #if $refBarcodeLocation.barcodeLocation == "idxfile":
6 --idxfile $refBarcodeLocation.idxfile
7 #else:
8 $refBarcodeLocation.EOL
9 #end if
10 > $output
11 </command>
12
13 <inputs>
14 <param format="txt" version="1.1" name="BARCODE" type="data" label="Barcodes to use" />
15 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" version="1.1" name="input" type="data" label="Library to split" />
16
17 <conditional name="refBarcodeLocation">
18 <param version="1.1" name="barcodeLocation" type="select" label="Barcodes found at">
19 <option value="bol">Start of sequence (5' end)</option>
20 <option value="eol">End of sequence (3' end)</option>
21 <option value="idxfile">Separate index file</option>
22 </param>
23 <when value="bol">
24 <param version="1.1" name="EOL" type="hidden" value="--bol" />
25 </when>
26 <when value="eol">
27 <param version="1.1" name="EOL" type="hidden" value="--eol" />
28 </when>
29 <when value="idxfile">
30 <param version="1.1" name="idxfile" type="data" format="fasta,fastq,fastqsanger" label="Select index read file" />
31 </when>
32 </conditional>
33
34 <param version="1.1" name="mismatches" type="integer" size="3" value="0" label="Number of allowed mismatches" />
35
36 <param version="1.1" name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" />
37
38 </inputs>
39
40 <tests>
41 <test>
42 <!-- Split a FASTQ file -->
43 <param version="1.1" name="BARCODE" value="fastx_barcode_splitter1.txt" />
44 <param version="1.1" name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
45 <param version="1.1" name="EOL" value="Start of sequence (5' end)" />
46 <param version="1.1" name="mismatches" value="2" />
47 <param version="1.1" name="partial" value="0" />
48 <output version="1.1" name="output" file="fastx_barcode_splitter1.out" />
49 </test>
50 </tests>
51
52 <outputs>
53 <data version="1.1" format="html" name="output" />
54 </outputs>
55 <help>
56
57 **What it does**
58
59 This tool splits a FASTQ or FASTA file into several files, using barcodes as the split criteria.
60
61 --------
62
63 **Barcode file Format**
64
65 Barcode files are simple text files.
66 Each line should contain an identifier (descriptive name for the barcode), and the barcode itself (A/C/G/T), separated by a TAB character.
67 Example::
68
69 #This line is a comment (starts with a 'number' sign)
70 BC1 GATCT
71 BC2 ATCGT
72 BC3 GTGAT
73 BC4 TGTCT
74
75 For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name).
76 Sequences matching the barcode will be stored in the appropriate file.
77
78 One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored.
79
80 The output of this tool is an HTML file, displaying the split counts and the file names.
81 In addition, each fastq file produced will be loaded into the galaxy history automatically.
82
83
84 ------
85
86 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
87
88 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
89
90 </help>
91 <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
92 </tool>