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comparison fastq_to_fasta.xml @ 0:3571553aeb20 draft

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author devteam
date Mon, 27 Jan 2014 09:27:22 -0500
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1 <tool id="fastq_to_fasta_python" name="FASTQ to FASTA" version="1.0.0">
2 <description>converter</description>
3 <requirements>
4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
5 </requirements>
6 <command interpreter="python">fastq_to_fasta.py '$input_file' '$output_file' '${input_file.extension[len( 'fastq' ):]}'</command>
7 <inputs>
8 <param name="input_file" type="data" format="fastq" label="FASTQ file to convert" />
9 </inputs>
10 <outputs>
11 <data name="output_file" format="fasta" />
12 </outputs>
13 <tests>
14 <!-- basic test -->
15 <test>
16 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
17 <output name="output_file" file="fastq_to_fasta_python_1.out" />
18 </test>
19 <!-- color space test -->
20 <test>
21 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" />
22 <output name="output_file" file="fastq_to_fasta_python_2.out" />
23 </test>
24 <!-- test of ignoring invalid score values: this input has ascii characters falling outside of illumina range, but they should not matter -->
25 <test>
26 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqillumina" />
27 <output name="output_file" file="fastq_to_fasta_python_1.out" />
28 </test>
29 </tests>
30 <help>
31 **What it does**
32
33 This tool converts FASTQ sequencing reads to FASTA sequences.
34
35 ------
36
37 **Citation**
38
39 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;`_
40
41
42 </help>
43 </tool>