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1 <tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA">
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2 <description>converter</description>
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3 <requirements>
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4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
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5 </requirements>
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6 <command>gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v
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7 #if $input.ext == "fastqsanger":
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8 -Q 33
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9 #end if
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10 </command>
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11
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12 <inputs>
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13 <param format="fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="FASTQ Library to convert" />
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14
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15 <param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases ">
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16 <option value="">yes</option>
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17 <option value="-n">no</option>
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18 </param>
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19
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20 <param name="RENAMESEQ" type="select" label="Rename sequence names in output file (reduces file size)">
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21 <option value="-r">yes</option>
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22 <option value="">no</option>
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23 </param>
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24
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25 </inputs>
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26
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27 <tests>
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28 <test>
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29 <!-- FASTQ-To-FASTA, keep N, don't rename -->
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30 <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
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31 <param name="SKIPN" value=""/>
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32 <param name="RENAMESEQ" value=""/>
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33 <output name="output" file="fastq_to_fasta1a.out" />
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34 </test>
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35 <test>
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36 <!-- FASTQ-To-FASTA, discard N, rename -->
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37 <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
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38 <param name="SKIPN" value="no"/>
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39 <param name="RENAMESEQ" value="yes"/>
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40 <output name="output" file="fastq_to_fasta1b.out" />
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41 </test>
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42 </tests>
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43
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44 <outputs>
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45 <data format="fasta" name="output" metadata_source="input" />
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46 </outputs>
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47
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48 <help>
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49
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50 **What it does**
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51
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52 This tool converts data from Solexa format to FASTA format (scroll down for format description).
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53
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54 --------
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55
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56 **Example**
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57
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58 The following data in Solexa-FASTQ format::
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59
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60 @CSHL_4_FC042GAMMII_2_1_517_596
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61 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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62 +CSHL_4_FC042GAMMII_2_1_517_596
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63 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
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64
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65 Will be converted to FASTA (with 'rename sequence names' = NO)::
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66
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67 >CSHL_4_FC042GAMMII_2_1_517_596
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68 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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69
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70 Will be converted to FASTA (with 'rename sequence names' = YES)::
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71
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72 >1
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73 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
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74
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75 ------
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76
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77 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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78
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79 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
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80 </help>
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81 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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82 </tool>
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