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1 <tool id="alignCustomAmplicon" name="Align Custom Amplicon" version="0.0.1">
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2 <description>align amplicon to reference with primers</description>
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3 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
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4 <requirements><requirement type="package" version="0.1.18">samtools</requirement></requirements>
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5 <requirements><requirement type="package" version="1.3.12">gzip</requirement></requirements>
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6 <requirements><requirement type="perl-module" version="0.42">Inline-CPP</requirement></requirements>
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7 <command interpreter="perl">
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8 alignCustomAmplicon.pl -s -r -p 4 -o $output $refFile.fields.path $read1 $read2 $primers
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9 </command>
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10
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11 <inputs>
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12 <param name="refFile" type="select" label="Select a reference genome">
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13 <options from_data_table="all_fasta">
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14 <filter type="sort_by" column="2" />
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15 <validator type="no_options" message="No indexes are available" />
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16 </options>
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17 </param>
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18 <param name="read1" type="data" format="fastqsanger,fastqillumina, fastq" label="FASTQ read 1 " help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" />
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19 <param name="read2" type="data" format="fastqsanger,fastqillumina, fastq" label="FASTQ read 2" help="FASTQ with either Sanger-scaled quality values (fastqsanger) or Illumina-scaled quality values (fastqillumina)" />
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20 <param name="primers" type="data" format="tabular" label="Primers" help="Primers location and length"/>
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21 </inputs>
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22
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23 <outputs>
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24 <data type="data" format="bam" name="output"/>
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25 </outputs>
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26
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27 <help>
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28
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29 .. class:: infomark
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30
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31 **What it does**
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32
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33 It is an amplicon aligner that uses primers for higher accuracy.
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34
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35 Reads with primers are aligned to the reference, then primers are discarded.
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36
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37 If both reads are long enough, they are aligned with the reference and a consensus alignment is generated.
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38
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39 Otherwise, each read is aligned separately.
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40
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41 Sequences with bad quality reads are discarded.
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42
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43
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44
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45 **Input**
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46
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47 ref:
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48
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49 Fasta file of ref gnome
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50
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51 read1:
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52
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53 Fastq file of left to right read
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54 (Can also be compressed [fastq.gz])
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55
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56 read2:
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57
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58 Fastq file of right to left read
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59 (Can also be compressed [fastq.gz])
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60
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61 primers:
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62
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63 Text file with primers name and length (see example)
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64
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65 Example primers format::
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66
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67 #Name_of_amplicon length_left length_right
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68 1:115256345-115256520 23 23
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69 1:115256436-115256606 25 22
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70 1:115256530-115256724 23 23
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71 1:115256532-115256723 23 23
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72 4:55151914-55152086 21 23
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73 4:55151935-55152132 20 23
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74 4:55151991-55152182 23 24
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75 4:55591944-55592136 23 24
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76 4:55592065-55592263 20 23
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77 4:55593504-55593674 24 25
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78 ...
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79
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80
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81 </help>
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82 </tool>
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