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comparison tools/fastq/fastq_combiner.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="fastq_combiner" name="Combine FASTA and QUAL" version="1.0.1">
2 <description>into FASTQ</description>
3 <command interpreter="python">fastq_combiner.py '$fasta_file' '${fasta_file.extension}' '$qual_file' '${qual_file.extension}' '$output_file' '$force_quality_encoding'</command>
4 <inputs>
5 <param name="fasta_file" type="data" format="fasta,csfasta" label="FASTA File" />
6 <param name="qual_file" type="data" format="qual" label="Quality Score File" optional="True" />
7 <param name="force_quality_encoding" type="select" label="Force Quality Score encoding">
8 <option value="None">Use Source Encoding</option>
9 <option value="ascii" selected="True">ASCII</option>
10 <option value="decimal">Decimal</option>
11 </param>
12 </inputs>
13 <outputs>
14 <data name="output_file" format="fastqsanger">
15 <change_format>
16 <when input_dataset="fasta_file" attribute="extension" value="csfasta" format="fastqcssanger" />
17 <when input_dataset="qual_file" attribute="extension" value="qualsolid" format="fastqcssanger" />
18 <when input_dataset="qual_file" attribute="extension" value="qualsolexa" format="fastqsolexa" />
19 <when input_dataset="qual_file" attribute="extension" value="qualillumina" format="fastqillumina" />
20 </change_format>
21 </data>
22 </outputs>
23 <tests>
24 <test>
25 <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" />
26 <param name="qual_file" value="s2fq_phiX.qualsolid" ftype="qualsolid" />
27 <param name="force_quality_encoding" value="None" />
28 <output name="output_file" file="combine_phiX_out_1.fastqcssanger" />
29 </test>
30 <test>
31 <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" />
32 <param name="qual_file" value="s2fq_phiX.qualsolid" ftype="qualsolid" />
33 <param name="force_quality_encoding" value="ascii" />
34 <output name="output_file" file="combine_phiX_out_2.fastqcssanger" />
35 </test>
36 <test>
37 <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" />
38 <param name="qual_file" value="fastq_combiner_in_1.qual454" ftype="qual454" />
39 <param name="force_quality_encoding" value="None" />
40 <output name="output_file" file="wrapping_as_sanger.fastqsanger" />
41 </test>
42 <test>
43 <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" />
44 <param name="qual_file" value="fastq_combiner_in_1.qual454" ftype="qual454" />
45 <param name="force_quality_encoding" value="decimal" />
46 <output name="output_file" file="wrapping_as_sanger_decimal.fastqsanger" />
47 </test>
48 <test>
49 <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" />
50 <param name="qual_file" />
51 <param name="force_quality_encoding" value="decimal" />
52 <output name="output_file" file="fastq_combiner_no_qual_decimal_out_1.fastqsanger" />
53 </test>
54 <test>
55 <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" />
56 <param name="qual_file" />
57 <param name="force_quality_encoding" value="ascii" />
58 <output name="output_file" file="fastq_combiner_no_qual_ascii_out_1.fastqcssanger" />
59 </test>
60 </tests>
61 <help>
62 **What it does**
63
64 This tool joins a FASTA file to a Quality Score file, creating a single FASTQ block for each read.
65
66 Specifying a set of quality scores is optional; when not provided, the output will be fastqsanger or fastqcssanger (when a csfasta is provided) with each quality score being the maximal allowed value (93).
67
68 Use this tool, for example, to convert 454-type output to FASTQ.
69
70 ------
71
72 **Citation**
73
74 If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20562416&gt;`_
75
76 </help>
77 </tool>