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annotate fastq_combiner.xml @ 3:5b1f1064c5df draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/galaxy_sequence_utils/fastq_combiner commit f2582539542b33240234e8ea6093e25d0aee9b6a
author devteam
date Sat, 30 Sep 2017 14:55:16 -0400
parents 02c665f7ac2b
children d0e9cb9ab094
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1 <tool id="fastq_combiner" name="Combine FASTA and QUAL" version="1.1.1">
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2 <description>into FASTQ</description>
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3 <requirements>
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4 <requirement type="package" version="1.1.1">galaxy_sequence_utils</requirement>
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5 </requirements>
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6 <command><![CDATA[
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7 gx-fastq-combiner '$fasta_file' '${fasta_file.extension}' '$qual_file' '${qual_file.extension}' '$output_file' $force_quality_encoding
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8 ]]></command>
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9 <inputs>
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10 <param name="fasta_file" type="data" format="fasta,csfasta" label="FASTA File" />
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11 <param name="qual_file" type="data" format="qual" optional="true" label="Quality Score File" />
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12 <param name="force_quality_encoding" type="select" label="Force Quality Score encoding">
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13 <option value="None">Use Source Encoding</option>
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14 <option value="ascii" selected="true">ASCII</option>
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15 <option value="decimal">Decimal</option>
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16 </param>
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17 </inputs>
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18 <outputs>
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19 <data name="output_file" format="fastqsanger">
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20 <change_format>
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21 <when input="fasta_file" value="csfasta" format="fastqcssanger" />
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22 <when input="qual_file" value="qualsolid" format="fastqcssanger" />
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23 <when input="qual_file" value="qualsolexa" format="fastqsolexa" />
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24 <when input="qual_file" value="qualillumina" format="fastqillumina" />
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25 </change_format>
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26 </data>
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" />
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31 <param name="qual_file" value="s2fq_phiX.qualsolid" ftype="qualsolid" />
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32 <param name="force_quality_encoding" value="None" />
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33 <output name="output_file" file="combine_phiX_out_1.fastqcssanger" />
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34 </test>
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35 <test>
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36 <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" />
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37 <param name="qual_file" value="s2fq_phiX.qualsolid" ftype="qualsolid" />
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38 <param name="force_quality_encoding" value="ascii" />
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39 <output name="output_file" file="combine_phiX_out_2.fastqcssanger" />
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40 </test>
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41 <test>
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42 <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" />
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43 <param name="qual_file" value="fastq_combiner_in_1.qual454" ftype="qual454" />
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44 <param name="force_quality_encoding" value="None" />
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45 <output name="output_file" file="wrapping_as_sanger.fastqsanger" />
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46 </test>
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47 <test>
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48 <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" />
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49 <param name="qual_file" value="fastq_combiner_in_1.qual454" ftype="qual454" />
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50 <param name="force_quality_encoding" value="decimal" />
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51 <output name="output_file" file="wrapping_as_sanger_decimal.fastqsanger" />
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52 </test>
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53 <test>
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54 <param name="fasta_file" value="fastq_combiner_in_1.fasta" ftype="fasta" />
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55 <param name="qual_file" />
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56 <param name="force_quality_encoding" value="decimal" />
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57 <output name="output_file" file="fastq_combiner_no_qual_decimal_out_1.fastqsanger" />
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58 </test>
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59 <test>
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60 <param name="fasta_file" value="s2fq_phiX.csfasta" ftype="csfasta" />
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61 <param name="qual_file" />
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62 <param name="force_quality_encoding" value="ascii" />
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63 <output name="output_file" file="fastq_combiner_no_qual_ascii_out_1.fastqcssanger" />
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64 </test>
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65 </tests>
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66 <help><![CDATA[
0
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67 **What it does**
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68
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69 This tool joins a FASTA file to a Quality Score file, creating a single FASTQ block for each read.
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70
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71 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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72
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73 Use this tool, for example, to convert 454-type output to FASTQ.
3
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74 ]]></help>
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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>
0
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78 </tool>