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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
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70 ------
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71
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72 **Citation**
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73
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74 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>`_
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75
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76 </help>
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77 </tool>
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