Mercurial > repos > fcaramia > custom_amplicon_alignment
comparison alignCustomAmplicon/alignCustomAmplicon_wrapper.xml @ 0:d32bddcff685 draft
Uploaded
| author | fcaramia |
|---|---|
| date | Wed, 09 Jan 2013 00:24:09 -0500 |
| parents | |
| children | 6a1b222df393 |
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| -1:000000000000 | 0:d32bddcff685 |
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| 1 <tool id="alignCustomAmplicon" name="Align Custom Amplicon" version="0.0.1"> | |
| 2 <description>align amplicon to reference with primers</description> | |
| 3 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> | |
| 4 <requirements><requirement type="package" version="0.1.18">samtools</requirement></requirements> | |
| 5 <requirements><requirement type="package" version="1.3.12">gzip</requirement></requirements> | |
| 6 <requirements><requirement type="perl-module" version="0.42">Inline-CPP</requirement></requirements> | |
| 7 <command interpreter="perl"> | |
| 8 alignCustomAmplicon.pl -s -r -p 4 -o $output $refFile.fields.path $read1 $read2 $primers | |
| 9 </command> | |
| 10 | |
| 11 <inputs> | |
| 12 <param name="refFile" type="select" label="Select a reference genome"> | |
| 13 <options from_data_table="all_fasta"> | |
| 14 <filter type="sort_by" column="2" /> | |
| 15 <validator type="no_options" message="No indexes are available" /> | |
| 16 </options> | |
| 17 </param> | |
| 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)" /> | |
| 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)" /> | |
| 20 <param name="primers" type="data" format="tabular" label="Primers" help="Primers location and length"/> | |
| 21 </inputs> | |
| 22 | |
| 23 <outputs> | |
| 24 <data type="data" format="bam" name="output"/> | |
| 25 </outputs> | |
| 26 | |
| 27 <help> | |
| 28 | |
| 29 .. class:: infomark | |
| 30 | |
| 31 **What it does** | |
| 32 | |
| 33 It is an amplicon aligner that uses primers for higher accuracy. | |
| 34 | |
| 35 Reads with primers are aligned to the reference, then primers are discarded. | |
| 36 | |
| 37 If both reads are long enough, they are aligned with the reference and a consensus alignment is generated. | |
| 38 | |
| 39 Otherwise, each read is aligned separately. | |
| 40 | |
| 41 Sequences with bad quality reads are discarded. | |
| 42 | |
| 43 | |
| 44 | |
| 45 **Input** | |
| 46 | |
| 47 ref: | |
| 48 | |
| 49 Fasta file of ref gnome | |
| 50 | |
| 51 read1: | |
| 52 | |
| 53 Fastq file of left to right read | |
| 54 (Can also be compressed [fastq.gz]) | |
| 55 | |
| 56 read2: | |
| 57 | |
| 58 Fastq file of right to left read | |
| 59 (Can also be compressed [fastq.gz]) | |
| 60 | |
| 61 primers: | |
| 62 | |
| 63 Text file with primers name and length (see example) | |
| 64 | |
| 65 Example primers format:: | |
| 66 | |
| 67 #Name_of_amplicon length_left length_right | |
| 68 1:115256345-115256520 23 23 | |
| 69 1:115256436-115256606 25 22 | |
| 70 1:115256530-115256724 23 23 | |
| 71 1:115256532-115256723 23 23 | |
| 72 4:55151914-55152086 21 23 | |
| 73 4:55151935-55152132 20 23 | |
| 74 4:55151991-55152182 23 24 | |
| 75 4:55591944-55592136 23 24 | |
| 76 4:55592065-55592263 20 23 | |
| 77 4:55593504-55593674 24 25 | |
| 78 ... | |
| 79 | |
| 80 | |
| 81 </help> | |
| 82 </tool> |