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