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comparison fastx_barcode_splitter.xml @ 3:3b0cd3132ddc draft

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:40:38 -0400
parents 1a20fbb8bad8
children e3d91cb9f196
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2:1a20fbb8bad8 3:3b0cd3132ddc
1 <tool id="cshl_fastx_barcode_splitter" version="1.0.0" name="Barcode Splitter"> 1 <tool id="cshl_fastx_barcode_splitter" version="1.0.0" name="Barcode Splitter">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement> 4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="bash">fastx_barcode_splitter_galaxy_wrapper.sh $BARCODE $input "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > $output </command> 6 <command interpreter="bash">fastx_barcode_splitter_galaxy_wrapper.sh '$BARCODE' '$input' "$input.name" "$output.files_path" --mismatches $mismatches --partial $partial $EOL > '$output' </command>
7 7
8 <inputs> 8 <inputs>
9 <param format="txt" name="BARCODE" type="data" label="Barcodes to use" /> 9 <param format="txt" name="BARCODE" type="data" label="Barcodes to use" />
10 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" /> 10 <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="Library to split" />
11 11
12 <param name="EOL" type="select" label="Barcodes found at"> 12 <param name="EOL" type="select" label="Barcodes found at">
13 <option value="--bol">Start of sequence (5' end)</option> 13 <option value="--bol">Start of sequence (5' end)</option>
14 <option value="--eol">End of sequence (3' end)</option> 14 <option value="--eol">End of sequence (3' end)</option>
15 </param> 15 </param>
16 16
17 <param name="mismatches" type="integer" size="3" value="2" label="Number of allowed mismatches" /> 17 <param name="mismatches" type="integer" value="2" label="Number of allowed mismatches" />
18
19 <param name="partial" type="integer" size="3" value="0" label="Number of allowed barcodes nucleotide deletions" />
20
21 </inputs>
22
23 <tests>
24 <test>
25 <!-- Split a FASTQ file -->
26 <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
27 <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
28 <param name="EOL" value="Start of sequence (5' end)" />
29 <param name="mismatches" value="2" />
30 <param name="partial" value="0" />
31 <param name="output" file="fastx_barcode_splitter1.out" />
32 </test>
33 </tests>
34 18
35 <outputs> 19 <param name="partial" type="integer" value="0" label="Number of allowed barcodes nucleotide deletions" />
36 <data format="html" name="output" /> 20 </inputs>
37 </outputs> 21 <outputs>
38 <help> 22 <data format="html" name="output" />
39 23 </outputs>
24 <tests>
25 <test>
26 <!-- Split a FASTQ file -->
27 <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
28 <param name="input" value="fastx_barcode_splitter1.fastq" ftype="fastqsolexa" />
29 <param name="EOL" value="Start of sequence (5' end)" />
30 <param name="mismatches" value="2" />
31 <param name="partial" value="0" />
32 <output name="output" file="fastx_barcode_splitter1.out" />
33 </test>
34 </tests>
35 <help>
40 **What it does** 36 **What it does**
41 37
42 This tool splits a Solexa library (FASTQ file) or a regular FASTA file into several files, using barcodes as the split criteria. 38 This tool splits a Solexa library (FASTQ file) or a regular FASTA file into several files, using barcodes as the split criteria.
43 39
44 -------- 40 --------
48 Barcode files are simple text files. 44 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. 45 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:: 46 Example::
51 47
52 #This line is a comment (starts with a 'number' sign) 48 #This line is a comment (starts with a 'number' sign)
53 BC1 GATCT 49 BC1 GATCT
54 BC2 ATCGT 50 BC2 ATCGT
55 BC3 GTGAT 51 BC3 GTGAT
56 BC4 TGTCT 52 BC4 TGTCT
57 53
58 For each barcode, a new FASTQ file will be created (with the barcode's identifier as part of the file name). 54 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. 55 Sequences matching the barcode will be stored in the appropriate file.
60 56
61 One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored. 57 One additional FASTQ file will be created (the 'unmatched' file), where sequences not matching any barcode will be stored.
62 58
70 ------ 66 ------
71 67
72 This tool is based on `FASTX-toolkit`__ by Assaf Gordon. 68 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
73 69
74 .. __: http://hannonlab.cshl.edu/fastx_toolkit/ 70 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
75 71 </help>
76 </help>
77 <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) --> 72 <!-- FASTX-barcode-splitter is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
78 </tool> 73 </tool>