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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 <requirements>
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4 <requirement type="package" version="1.0.0">galaxy_sequence_utils</requirement>
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5 </requirements>
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6 <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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7 <inputs>
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8 <param name="input1_file" type="data" format="fastqsanger,fastqcssanger" label="Left-hand mates" />
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9 <param name="input2_file" type="data" format="fastqsanger,fastqcssanger" label="Right-hand mates" />
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10 </inputs>
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11 <outputs>
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12 <!-- $input1_file.name = filename , e.g. paired_end_2_errors.fastqsanger -->
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13 <!-- $input1_file.id = ID , e.g. 10 -->
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14 <!-- $input1_file.hid = history ID, e.g. 5 -->
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15 <data name="outfile_pairs" format="input" label="FASTQ interlacer pairs from data ${input1_file.hid} and data ${input2_file.hid}"/>
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16 <data name="outfile_singles" format="input" label="FASTQ interlacer singles from data ${input1_file.hid} and data ${input2_file.hid}"/>
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="input1_file" value="paired_end_1.fastqsanger" ftype="fastqsanger" />
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21 <param name="input2_file" value="paired_end_2.fastqsanger" ftype="fastqsanger" />
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22 <output name="outfile_pairs" file="paired_end_merged.fastqsanger" />
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23 <output name="outfile_singles" file="paired_end_merged_singles.fastqsanger" />
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24 </test>
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25 <test>
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26 <param name="input1_file" value="paired_end_1_errors.fastqsanger" ftype="fastqsanger" />
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27 <param name="input2_file" value="paired_end_2_errors.fastqsanger" ftype="fastqsanger" />
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28 <output name="outfile_pairs" file="paired_end_merged_cleaned.fastqsanger" />
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29 <output name="outfile_singles" file="paired_end_merged_cleaned_singles.fastqsanger" />
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30 </test>
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31 </tests>
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32 <help>
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33 **What it does**
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34
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35 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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36
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37 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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38
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39 -----
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40
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41 **Input**
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42
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43 Left-hand mates, for example::
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44
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45 @1539:931/1
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46 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
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47 +1539:931/1
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48 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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49
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50 Right-hand mates, for example::
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51
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52 @1539:931/2
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53 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
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54 +1539:931/2
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55 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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56
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57 -----
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58
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59 **Output**
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60
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61 A multiple-fastq file containing interlaced left and right paired reads::
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62
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63 @1539:931/1
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64 ACTTCCCGCGCGTGAAGGCGCCGGCAAACGAGGCTCGGGAAGGGGCTCCCG
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65 +1539:931/1
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66 BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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67 @1539:931/2
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68 CGCCATTCCGAATCGTAGTTGTCGGCGTCTTCCAGTGCGGCAAGGCATCGT
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69 +1539:931/2
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70 WNUUZ\P^`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
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71
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72 A multiple-fastq file containing reads that have no mate is also produced.
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73
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74 </help>
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75 </tool>
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