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0
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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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1
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3 <requirements>
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4 <requirement type="package" version="1.56.0">picard</requirement>
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5 <requirement type="package" version="0.1.18">samtools</requirement>
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6 <requirement type="package" version="1.3.12">gzip</requirement>
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7 <requirement type="perl-module" version="0.42">Inline-CPP</requirement>
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8 </requirements>
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0
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9 <command interpreter="perl">
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10 alignCustomAmplicon.pl -s -r -p 4 -o $output $refFile.fields.path $read1 $read2 $primers
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2
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11 -j "\$JAVA_JAR_PATH/MergeSamFiles.jar"
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0
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12 </command>
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13
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14 <inputs>
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15 <param name="refFile" type="select" label="Select a reference genome">
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16 <options from_data_table="all_fasta">
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17 <filter type="sort_by" column="2" />
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18 <validator type="no_options" message="No indexes are available" />
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19 </options>
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20 </param>
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21 <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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22 <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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23 <param name="primers" type="data" format="tabular" label="Primers" help="Primers location and length"/>
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24 </inputs>
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25
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26 <outputs>
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27 <data type="data" format="bam" name="output"/>
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28 </outputs>
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29
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30 <help>
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31
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32 .. class:: infomark
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33
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34 **What it does**
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35
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36 It is an amplicon aligner that uses primers for higher accuracy.
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37
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38 Reads with primers are aligned to the reference, then primers are discarded.
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39
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40 If both reads are long enough, they are aligned with the reference and a consensus alignment is generated.
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41
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42 Otherwise, each read is aligned separately.
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43
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44 Sequences with bad quality reads are discarded.
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45
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46
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47
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48 **Input**
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49
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50 ref:
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51
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52 Fasta file of ref gnome
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53
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54 read1:
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55
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56 Fastq file of left to right read
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57 (Can also be compressed [fastq.gz])
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58
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59 read2:
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60
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61 Fastq file of right to left read
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62 (Can also be compressed [fastq.gz])
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63
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64 primers:
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65
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66 Text file with primers name and length (see example)
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67
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68 Example primers format::
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69
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70 #Name_of_amplicon length_left length_right
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71 1:115256345-115256520 23 23
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72 1:115256436-115256606 25 22
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73 1:115256530-115256724 23 23
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74 1:115256532-115256723 23 23
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75 4:55151914-55152086 21 23
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76 4:55151935-55152132 20 23
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77 4:55151991-55152182 23 24
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78 4:55591944-55592136 23 24
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79 4:55592065-55592263 20 23
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80 4:55593504-55593674 24 25
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81 ...
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82
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83
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84 </help>
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85 </tool>
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