[2] | 1 | <tool id="fastq_combiner" name="Combine FASTA and QUAL" version="1.0.1"> |
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| 2 | <description>into FASTQ</description> |
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| 3 | <command interpreter="python">fastq_combiner.py '$fasta_file' '${fasta_file.extension}' '$qual_file' '${qual_file.extension}' '$output_file' '$force_quality_encoding'</command> |
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| 4 | <inputs> |
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| 5 | <param name="fasta_file" type="data" format="fasta,csfasta" label="FASTA File" /> |
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| 6 | <param name="qual_file" type="data" format="qual" label="Quality Score File" optional="True" /> |
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| 7 | <param name="force_quality_encoding" type="select" label="Force Quality Score encoding"> |
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| 8 | <option value="None">Use Source Encoding</option> |
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| 9 | <option value="ascii" selected="True">ASCII</option> |
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| 10 | <option value="decimal">Decimal</option> |
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| 11 | </param> |
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| 12 | </inputs> |
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| 13 | <outputs> |
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| 14 | <data name="output_file" format="fastqsanger"> |
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| 15 | <change_format> |
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| 16 | <when input_dataset="fasta_file" attribute="extension" value="csfasta" format="fastqcssanger" /> |
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| 17 | <when input_dataset="qual_file" attribute="extension" value="qualsolid" format="fastqcssanger" /> |
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| 18 | <when input_dataset="qual_file" attribute="extension" value="qualsolexa" format="fastqsolexa" /> |
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| 19 | <when input_dataset="qual_file" attribute="extension" value="qualillumina" format="fastqillumina" /> |
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| 20 | </change_format> |
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| 21 | </data> |
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| 22 | </outputs> |
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| 23 | <tests> |
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| 24 | <test> |
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| 25 | <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" /> |
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| 26 | <param name="qual_file" value="s2fq_phiX.qualsolid" ftype="qualsolid" /> |
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| 27 | <param name="force_quality_encoding" value="None" /> |
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| 28 | <output name="output_file" file="combine_phiX_out_1.fastqcssanger" /> |
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| 29 | </test> |
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| 30 | <test> |
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| 31 | <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" /> |
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| 32 | <param name="qual_file" value="s2fq_phiX.qualsolid" ftype="qualsolid" /> |
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| 33 | <param name="force_quality_encoding" value="ascii" /> |
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| 34 | <output name="output_file" file="combine_phiX_out_2.fastqcssanger" /> |
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| 35 | </test> |
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| 36 | <test> |
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| 37 | <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" /> |
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| 38 | <param name="qual_file" value="fastq_combiner_in_1.qual454" ftype="qual454" /> |
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| 39 | <param name="force_quality_encoding" value="None" /> |
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| 40 | <output name="output_file" file="wrapping_as_sanger.fastqsanger" /> |
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| 41 | </test> |
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| 42 | <test> |
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| 43 | <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" /> |
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| 44 | <param name="qual_file" value="fastq_combiner_in_1.qual454" ftype="qual454" /> |
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| 45 | <param name="force_quality_encoding" value="decimal" /> |
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| 46 | <output name="output_file" file="wrapping_as_sanger_decimal.fastqsanger" /> |
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| 47 | </test> |
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| 48 | <test> |
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| 49 | <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" /> |
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| 50 | <param name="qual_file" /> |
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| 51 | <param name="force_quality_encoding" value="decimal" /> |
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| 52 | <output name="output_file" file="fastq_combiner_no_qual_decimal_out_1.fastqsanger" /> |
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| 53 | </test> |
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| 54 | <test> |
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| 55 | <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" /> |
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| 56 | <param name="qual_file" /> |
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| 57 | <param name="force_quality_encoding" value="ascii" /> |
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| 58 | <output name="output_file" file="fastq_combiner_no_qual_ascii_out_1.fastqcssanger" /> |
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| 59 | </test> |
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| 60 | </tests> |
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| 61 | <help> |
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| 62 | **What it does** |
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| 63 | |
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| 64 | This tool joins a FASTA file to a Quality Score file, creating a single FASTQ block for each read. |
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| 65 | |
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| 66 | Specifying a set of quality scores is optional; when not provided, the output will be fastqsanger or fastqcssanger (when a csfasta is provided) with each quality score being the maximal allowed value (93). |
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| 67 | |
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| 68 | Use this tool, for example, to convert 454-type output to FASTQ. |
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| 69 | </help> |
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| 70 | </tool> |
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