Mercurial > repos > devteam > fastqtofasta
view fastq_to_fasta.xml @ 1:723b5b38d88a draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastqtofasta commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
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date | Wed, 11 Nov 2015 12:43:11 -0500 |
parents | 3571553aeb20 |
children | 4844c1810c16 |
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<tool id="fastq_to_fasta_python" name="FASTQ to FASTA" version="1.0.0"> <description>converter</description> <requirements> <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement> </requirements> <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. </help> <citations> <citation type="doi">10.1093/bioinformatics/btq281</citation> </citations> </tool>