Mercurial > repos > fcaramia > custom_amplicon_alignment
view alignCustomAmplicon/alignCustomAmplicon_wrapper.xml @ 3:a72948f2c8c7 draft
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author | fcaramia |
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date | Wed, 09 Jan 2013 00:36:07 -0500 |
parents | 413ba6d9cc46 |
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<tool id="alignCustomAmplicon" name="Align Custom Amplicon" version="0.0.1"> <description>align amplicon to reference with primers</description> <requirements> <requirement type="package" version="1.56.0">picard</requirement> <requirement type="package" version="0.1.18">samtools</requirement> <requirement type="package" version="1.3.12">gzip</requirement> <requirement type="perl-module" version="0.42">Inline-CPP</requirement> </requirements> <command interpreter="perl"> alignCustomAmplicon.pl -s -r -p 4 -o $output $refFile.fields.path $read1 $read2 $primers -j "\$JAVA_JAR_PATH/MergeSamFiles.jar" </command> <inputs> <param name="refFile" type="select" label="Select a reference genome"> <options from_data_table="all_fasta"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No indexes are available" /> </options> </param> <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)" /> <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)" /> <param name="primers" type="data" format="tabular" label="Primers" help="Primers location and length"/> </inputs> <outputs> <data type="data" format="bam" name="output"/> </outputs> <help> .. class:: infomark **What it does** It is an amplicon aligner that uses primers for higher accuracy. Reads with primers are aligned to the reference, then primers are discarded. If both reads are long enough, they are aligned with the reference and a consensus alignment is generated. Otherwise, each read is aligned separately. Sequences with bad quality reads are discarded. **Input** ref: Fasta file of ref gnome read1: Fastq file of left to right read (Can also be compressed [fastq.gz]) read2: Fastq file of right to left read (Can also be compressed [fastq.gz]) primers: Text file with primers name and length (see example) Example primers format:: #Name_of_amplicon length_left length_right 1:115256345-115256520 23 23 1:115256436-115256606 25 22 1:115256530-115256724 23 23 1:115256532-115256723 23 23 4:55151914-55152086 21 23 4:55151935-55152132 20 23 4:55151991-55152182 23 24 4:55591944-55592136 23 24 4:55592065-55592263 20 23 4:55593504-55593674 24 25 ... </help> </tool>