Mercurial > repos > bgruening > nanopolish_variants
diff nanopolish_variants.xml @ 0:639b3a5bb415 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
author | bgruening |
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date | Wed, 30 May 2018 11:56:35 -0400 |
parents | |
children | 1ebed8b65752 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nanopolish_variants.xml Wed May 30 11:56:35 2018 -0400 @@ -0,0 +1,163 @@ +<tool id="nanopolish_variants" name="Nanopolish variants" version="0.1.0"> + <description>- Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$input_merged' reads.fasta && + + #if $input_reads_raw.extension == 'fast5': + mkdir fast5_files && ln -s '$input_reads_raw' fast5_files/read1.fast5 && + #else + ln -s '$input_reads_raw' fast5_files.tar.gz && + mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files && + #end if + + nanopolish index -d fast5_files/ reads.fasta && + ln -s '$b' reads.bam && + ln -s '${b.metadata.bam_index}' reads.bam.bai && + ln -s '$g' genome.fa && + + nanopolish variants + -r reads.fasta + -b reads.bam + -g genome.fa + -o variants.vcf + #if $consensus: + --consensus polished.fa + #end if + + $snps + $verbose + $homopolymer + $faster + $all_bases + + -m $min_candidate_frequency + -d $min_candidate_depth + -x $max_haplotypes + --max-rounds $max_rounds + #if $ploidy != -1: + --ploidy $ploidy + #end if + + #if $w and str($w).strip(): + -w "${w}" + #end if + #if $methylation_aware and str($methylation_aware).strip(): + -q "${methylation_aware}" + #end if + + #if $adv.input_events_bam: + -e '$adv.input_events_bam' + #end if + #if $adv.input_genotype: + --genotype '$adv.input_genotype' + #end if + #if $adv.input_candidates: + -c '$adv.input_candidates' + #end if + #if $adv.input_alt_bc_bam: + -a '$adv.input_alt_bc_bam' + #end if + #if $adv.input_models_fofn: + --models-fofn '$input_models_fofn' + #end if + + + + ]]></command> + <inputs> + <!-- index inputs --> + <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/> + <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz" label="Flat archive file of raw fast5 files"/> + + <!-- variants consensus inputs --> + <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" /> + <param type="data" argument="-g" format="fasta" label="The reference genome"/> + + <section name="adv" title="Optional data inputs"> + <!-- optional inputs --> + <param type="data" name="input_seq_summary" format="txt" optional="true" label="Sequencing summary file from albacore" help="(-s)"/> + <param type="data" name="input_events_bam" format="bam" optional="true" label="Events aligned to the reference genome" help="(-e)" /> + <param type="data" name="input_genotype" format="vcf" optional="true" label="Call genotypes for the variants in the vcf file" help="(--genotype)" /> + <param type="data" name="input_candidates" format="vcf" optional="true" + label="Use variant candidates, rather than discovering them from aligned reads" help="(-c)" /> + <param type="data" name="input_alt_bc_bam" format="bam" optional="true" label="Alternative basecaller used that does not output event annotations" help="(-a)" /> + <param type="data" name="input_models_fofn" format="txt" optional="true" label="Read alternative k-mer models" help="(--models-fofn)" /> + </section> + + <!-- optional params --> + <!-- optional params --> + <param argument="-w" type="text" optional="true" + label="find variants in window of region chromsome:start-end" /> + <param name="methylation_aware" type="text" optional="true" label="methylation aware polishing and test motifs given" help="(-q)"/> + <param name="min_candidate_frequency" type="float" optional="true" value="0.2" label="Extarct if the variant frequency is at least F" help="(-m)"/> + <param name="min_candidate_depth" type="integer" optional="true" value="20" label="Extarct if the depth is at least D" help="(-d)"/> + <param name="max_haplotypes" type="integer" optional="true" value="1000" label="Consider at most N haplotype combinations" help="(-x)"/> + <param name="max_rounds" type="integer" optional="true" value="50" label="Perform N rounds of consensus sequence improvement" help="(--max_rounds)"/> + <param name="ploidy" type="integer" optional="true" value="-1" label="The ploidy level of the sequenced genome. -1:disabled" help="(-p)"/> + + <!-- optional flags --> + <param argument="--consensus" type="boolean" truevalue="--consensus" falsevalue="" checked="true" label="Consensus calling mode and output polished sequence" /> + <param argument="--snps" type="boolean" truevalue="--snps" falsevalue="" checked="false" label="only call SNPs"/> + <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="verbose output"/> + <param name="homopolymer" type="boolean" argument="--fix-homopolymers" truevalue="--fix-homopolymers" falsevalue="" checked="false" label="homopolymer caller" /> + <param argument="--faster" type="boolean" truevalue="--faster" falsevalue="" checked="false" + label="speedup while slightly reducing consensus accuracy"/> + <param name="all_bases" type="boolean" argument="--calculate-all-support" truevalue="--calculate-all-support" falsevalue="" checked="false" + label="calculate the support of the 3 other possible bases" /> + </inputs> + + <outputs> + <!-- variants consensus outputs --> + <data name="output_polished" format="fasta" from_work_dir="polished.fa" label="polished sequence by consensus calling mode" /> + <data name="output_variants" format="vcf" from_work_dir="variants.vcf" label="Computed variants"/> + </outputs> + <tests> + <test> + <!-- index test --> + <param name="input_merged" ftype="fasta" value="reads.fasta" /> + <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> + + <!-- variants consensus test --> + <param name="b" value="reads.sorted.bam" /> + <param name="g" value="draft.fa" /> + <param name="w" value="tig00000001:200000-202000" /> + + <output name="output_polished" file="polished.fa" /> + <output name="output_variants" file="variants.vcf"/> + </test> + <test> + <!-- index test --> + <param name="input_merged" ftype="fasta" value="reads.fasta" /> + <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> + + <!-- variants consensus test --> + <param name="b" value="reads.sorted.bam" /> + <param name="g" value="draft.fa" /> + <param name="w" value="tig00000001:200000-202000" /> + <param name="ploidy" value="2" /> + <param name="snps" value="true" /> + <param name="faster" value="true" /> + <param name="all_bases" value="true" /> + <param name="consensus" value="false" /> + <output name="output_polished" file="t2-polished.fa" /> + <output name="output_variants" file="t2-variants.vcf"/> + </test> + + </tests> + <help><![CDATA[ + + Build an index mapping from basecalled reads to the signals measured by the sequencer + and + Find SNPs using a signal-level HMM + + Tutorial and manual available at: + http://nanopolish.readthedocs.io/en/latest/quickstart_consensus.html + + + ]]></help> + <expand macro="citations" /> +</tool>