Mercurial > repos > devteam > fastq_combiner
annotate fastq_combiner.xml @ 1:02c665f7ac2b draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:42:26 -0400 |
| parents | 82f441097692 |
| children | 5b1f1064c5df |
| rev | line source |
|---|---|
| 0 | 1 <tool id="fastq_combiner" name="Combine FASTA and QUAL" version="1.0.1"> |
| 2 <description>into FASTQ</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python">fastq_combiner.py '$fasta_file' '${fasta_file.extension}' '$qual_file' '${qual_file.extension}' '$output_file' '$force_quality_encoding'</command> | |
| 7 <inputs> | |
| 8 <param name="fasta_file" type="data" format="fasta,csfasta" label="FASTA File" /> | |
| 9 <param name="qual_file" type="data" format="qual" label="Quality Score File" optional="True" /> | |
| 10 <param name="force_quality_encoding" type="select" label="Force Quality Score encoding"> | |
| 11 <option value="None">Use Source Encoding</option> | |
| 12 <option value="ascii" selected="True">ASCII</option> | |
| 13 <option value="decimal">Decimal</option> | |
| 14 </param> | |
| 15 </inputs> | |
| 16 <outputs> | |
| 17 <data name="output_file" format="fastqsanger"> | |
| 18 <change_format> | |
| 19 <when input_dataset="fasta_file" attribute="extension" value="csfasta" format="fastqcssanger" /> | |
| 20 <when input_dataset="qual_file" attribute="extension" value="qualsolid" format="fastqcssanger" /> | |
| 21 <when input_dataset="qual_file" attribute="extension" value="qualsolexa" format="fastqsolexa" /> | |
| 22 <when input_dataset="qual_file" attribute="extension" value="qualillumina" format="fastqillumina" /> | |
| 23 </change_format> | |
| 24 </data> | |
| 25 </outputs> | |
| 26 <tests> | |
| 27 <test> | |
| 28 <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" /> | |
| 29 <param name="qual_file" value="s2fq_phiX.qualsolid" ftype="qualsolid" /> | |
| 30 <param name="force_quality_encoding" value="None" /> | |
| 31 <output name="output_file" file="combine_phiX_out_1.fastqcssanger" /> | |
| 32 </test> | |
| 33 <test> | |
| 34 <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" /> | |
| 35 <param name="qual_file" value="s2fq_phiX.qualsolid" ftype="qualsolid" /> | |
| 36 <param name="force_quality_encoding" value="ascii" /> | |
| 37 <output name="output_file" file="combine_phiX_out_2.fastqcssanger" /> | |
| 38 </test> | |
| 39 <test> | |
| 40 <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" /> | |
| 41 <param name="qual_file" value="fastq_combiner_in_1.qual454" ftype="qual454" /> | |
| 42 <param name="force_quality_encoding" value="None" /> | |
| 43 <output name="output_file" file="wrapping_as_sanger.fastqsanger" /> | |
| 44 </test> | |
| 45 <test> | |
| 46 <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" /> | |
| 47 <param name="qual_file" value="fastq_combiner_in_1.qual454" ftype="qual454" /> | |
| 48 <param name="force_quality_encoding" value="decimal" /> | |
| 49 <output name="output_file" file="wrapping_as_sanger_decimal.fastqsanger" /> | |
| 50 </test> | |
| 51 <test> | |
| 52 <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" /> | |
| 53 <param name="qual_file" /> | |
| 54 <param name="force_quality_encoding" value="decimal" /> | |
| 55 <output name="output_file" file="fastq_combiner_no_qual_decimal_out_1.fastqsanger" /> | |
| 56 </test> | |
| 57 <test> | |
| 58 <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" /> | |
| 59 <param name="qual_file" /> | |
| 60 <param name="force_quality_encoding" value="ascii" /> | |
| 61 <output name="output_file" file="fastq_combiner_no_qual_ascii_out_1.fastqcssanger" /> | |
| 62 </test> | |
| 63 </tests> | |
| 64 <help> | |
| 65 **What it does** | |
| 66 | |
| 67 This tool joins a FASTA file to a Quality Score file, creating a single FASTQ block for each read. | |
| 68 | |
| 69 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). | |
| 70 | |
| 71 Use this tool, for example, to convert 454-type output to FASTQ. | |
| 72 | |
| 73 </help> | |
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74 |
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75 <citations> |
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76 <citation type="doi">10.1093/bioinformatics/btq281</citation> |
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77 </citations> |
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78 |
| 0 | 79 </tool> |