/tools/fastq/fastq_to_fasta.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 40 lines · 31 code · 6 blank · 3 comment · 0 complexity · 6573cdfc5a7163cdab95a4364ba5f771 MD5 · raw file
- <tool id="fastq_to_fasta_python" name="FASTQ to FASTA" version="1.0.0">
- <description>converter</description>
- <command interpreter="python">fastq_to_fasta.py '$input_file' '$output_file' '${input_file.extension[len( 'fastq' ):]}'</command>
- <inputs>
- <param name="input_file" type="data" format="fastq" label="FASTQ file to convert" />
- </inputs>
- <outputs>
- <data name="output_file" format="fasta" />
- </outputs>
- <tests>
- <!-- basic test -->
- <test>
- <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
- <output name="output_file" file="fastq_to_fasta_python_1.out" />
- </test>
- <!-- color space test -->
- <test>
- <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" />
- <output name="output_file" file="fastq_to_fasta_python_2.out" />
- </test>
- <!-- test of ignoring invalid score values: this input has ascii characters falling outside of illumina range, but they should not matter -->
- <test>
- <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqillumina" />
- <output name="output_file" file="fastq_to_fasta_python_1.out" />
- </test>
- </tests>
- <help>
- **What it does**
- This tool converts FASTQ sequencing reads to FASTA sequences.
- ------
- **Citation**
- 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. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_
- </help>
- </tool>