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1 <tool id="fastq_paired_end_interlacer" name="FASTQ 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_interlacer.py '$input1_file' '${input1_file.extension[len( 'fastq' ):]}' '$input2_file' '${input2_file.extension[len( 'fastq' ):]}' '$outfile_pairs' '$outfile_singles'</command>
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4 <inputs>
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5 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger" label="Left-hand mates" />
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6 <param name="input2_file" type="data" format="fastqsanger,fastqcssanger" label="Right-hand mates" />
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7 </inputs>
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8 <outputs>
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9 <!-- $input1_file.name = filename , e.g. paired_end_2_errors.fastqsanger -->
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10 <!-- $input1_file.id = ID , e.g. 10 -->
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11 <!-- $input1_file.hid = history ID, e.g. 5 -->
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12 <data name="outfile_pairs" format="input" label="FASTQ interlacer pairs from data ${input1_file.hid} and data ${input2_file.hid}"/>
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13 <data name="outfile_singles" format="input" label="FASTQ interlacer singles from data ${input1_file.hid} and data ${input2_file.hid}"/>
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14 </outputs>
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15 <tests>
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16 <test>
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17 <param name="input1_file" value="paired_end_1.fastqsanger" ftype="fastqsanger" />
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18 <param name="input2_file" value="paired_end_2.fastqsanger" ftype="fastqsanger" />
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19 <output name="outfile_pairs" file="paired_end_merged.fastqsanger" />
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20 <output name="outfile_singles" file="paired_end_merged_singles.fastqsanger" />
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21 </test>
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22 <test>
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23 <param name="input1_file" value="paired_end_1_errors.fastqsanger" ftype="fastqsanger" />
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24 <param name="input2_file" value="paired_end_2_errors.fastqsanger" ftype="fastqsanger" />
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25 <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" />
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26 <output name="outfile_singles" file="paired_end_merged_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 This tool joins paired end FASTQ reads from two separate files, one with the left mates and one with the right mates, into a single files where left mates alternate with their right mates. The join is performed using sequence identifiers, allowing the two files to contain differing ordering. If a sequence identifier does not appear in both files, it is included in a separate file.
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33
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34 Sequence identifiers with /1 and /2 appended override the left-hand and right-hand designation; i.e. if the reads end with /1 and /2, the read containing /1 will be used as the left-hand read and the read containing /2 will be used as the right-hand read. Sequences without this designation will follow the left-hand and right-hand settings set by the user.
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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 Left-hand mates, 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
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47 Right-hand mates, for example::
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48
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49 @1539:931/2
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50 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
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51 +1539:931/2
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52 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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53
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54 -----
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55
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56 **Output**
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57
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58 A multiple-fastq file containing interlaced left and right paired reads::
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59
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60 @1539:931/1
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61 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
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62 +1539:931/1
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63 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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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 A multiple-fastq file containing reads that have no mate is also produced.
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70
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71 </help>
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72 </tool>
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