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1 <tool id="fastq_paired_end_deinterlacer" name="FASTQ de-interlacer" version="1.1">
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2 <description>on paired end reads</description>
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3 <command interpreter="python">fastq_paired_end_deinterlacer.py '$input_file' '${input_file.extension[len( 'fastq' ):]}' '$output1_pairs_file' '$output2_pairs_file' '$output1_singles_file' '$output2_singles_file'</command>
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4 <inputs>
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5 <param name="input_file" type="data" format="fastqsanger,fastqcssanger" label="FASTQ reads" />
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6 </inputs>
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7 <outputs>
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8 <data name="output1_pairs_file" format="input" label="FASTQ de-interlacer left mates from data ${input_file.hid}" />
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9 <data name="output2_pairs_file" format="input" label="FASTQ de-interlacer right mates from data ${input_file.hid}"/>
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10 <data name="output1_singles_file" format="input" label="FASTQ de-interlacer left singles from data ${input_file.hid}"/>
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11 <data name="output2_singles_file" format="input" label="FASTQ de-interlacer right singles from data ${input_file.hid}"/>
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12 </outputs>
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13 <tests>
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14 <test>
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15 <param name="input_file" value="paired_end_merged.fastqsanger" ftype="fastqsanger" />
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16 <output name="output1_pairs_file" file="paired_end_1.fastqsanger" />
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17 <output name="output2_pairs_file" file="paired_end_2.fastqsanger" />
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18 <output name="output1_singles_file" file="paired_end_1_singles.fastqsanger" />
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19 <output name="output2_singles_file" file="paired_end_2_singles.fastqsanger" />
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20 </test>
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21 <test>
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22 <param name="input_file" value="paired_end_merged_errors.fastqsanger" ftype="fastqsanger" />
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23 <output name="output1_pairs_file" file="paired_end_1_cleaned.fastqsanger" />
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24 <output name="output2_pairs_file" file="paired_end_2_cleaned.fastqsanger" />
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25 <output name="output1_singles_file" file="paired_end_1_cleaned_singles.fastqsanger" />
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26 <output name="output2_singles_file" file="paired_end_2_cleaned_singles.fastqsanger" />
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27 </test>
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28 </tests>
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29 <help>
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30 **What it does**
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31
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32 De-interlaces a single fastq dataset representing paired-end run into two fastq datasets containing only the first or second mate read. Reads without mate are saved in separate output files.
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33
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34 Sequence identifiers for paired-end reads must follow the /1 and /2 convention.
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35
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36 -----
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37
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38 **Input**
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39
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40 A multiple-fastq file containing paired-end reads, for example::
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41
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42 @1539:931/1
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43 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
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44 +1539:931/1
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45 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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46 @1539:931/2
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47 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
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48 +1539:931/2
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49 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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50
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51 -----
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52
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53 **Output**
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54
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55 Multi-fastq file with left-hand mate only::
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56
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57 @1539:931/1
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58 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
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59 +1539:931/1
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60 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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61
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62 Multi-fastq file with right-hand mate only::
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63
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64 @1539:931/2
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65 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
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66 +1539:931/2
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67 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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68
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69 </help>
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70 </tool>
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