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