Mercurial > repos > dsobral > breseq
changeset 10:e21c4ceb0039 draft default tip
Uploaded
author | dsobral |
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date | Sat, 03 Mar 2018 11:47:47 -0500 |
parents | f8198c2ae33d |
children | |
files | breseq.xml |
diffstat | 1 files changed, 160 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/breseq.xml Sat Mar 03 11:47:47 2018 -0500 @@ -0,0 +1,160 @@ +<tool id="breseq" name="Breseq Variant Report" version="0.31.1" hidden="false"> + <description>Runs Breseq software on a set of fastq files</description> + + <requirements> + <requirement type="package" version="0.31.1">breseq</requirement> + </requirements> + + <command interpreter="python"> + breseq_wrapper.py + + $outfile + $outfile.files_path + + --num-processors \${GALAXY_SLOTS:-4} + + #if str($reference.source) == "history": + #for $i, $s in enumerate( $reference.ref_series ) + -r $s.own_genome + #end for + #else: + -r $reference.fixed_genome.fields.path + #end if + #for $i, $s in enumerate( $read_series ) + ${s.input} + #end for + + #if str($polymorphism.selection) == "yes": + --polymorphism-prediction + --polymorphism-reject-indel-homopolymer-length $polymorphism.indel_homopolymer_length + --polymorphism-reject-surrounding-homopolymer-length $polymorphism.surrounding_homopolymer_length + --polymorphism-minimum-coverage-each-strand $polymorphism.strand_coverage + --polymorphism-bias-cutoff $polymorphism.bias_pvalue + #end if + + #if str($junction_reference.selection) == "yes": + #for $i, $s in enumerate( $junction_reference.j_series ) + --junction-only-reference $s.jc_genome + #end for + #end if + + ${cnv_evidence} + + -b $minqvalue + + </command> + + <stdio> + <exit_code range="1:" level="fatal" description="Fatal ERROR exit code greater than 1" /> + </stdio> + + <inputs> + <!-- reference genome --> + <conditional name="reference"> + <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in genome?" > + <option value="indexed">Use a built-in genome</option> + <option value="history">Use one from the history</option> + </param> + <when value="indexed"> + <param name="fixed_genome" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Bioinformatics team"> + <options from_data_table="genbank_files"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options> + </param> + </when> + <when value="history"> + <!-- <param name="own_genome" type="data" label="Select the reference genome (fasta or genbank)" /> --> + <repeat name="ref_series" title="Reference Genome" min="1"> + <param name="own_genome" type="data" label="Select the reference genome (fasta or genbank)" /> + </repeat> + </when> + </conditional> + + + <!-- input Fastq files --> + <repeat name="read_series" title="Read File" min="1"> + <param name="input" type="data" format="fastq" label="Dataset" /> + </repeat> + + + <!-- select polymorphism --> + <conditional name="polymorphism"> + <param name="selection" type="select" label="Perform polimorphism detection" help="Do you want to perform polimorphism detection in a population"> + <option value="no">Do not perform polymorphism detection</option> + <option value="yes">Perform polymorphism detection</option> + </param> + <when value="yes"> + <param name="indel_homopolymer_length" type="integer" value="0" label="Reject insertion/deletion polymorphisms due to homopolymer repeats with this length or greater" /> + <param name="surrounding_homopolymer_length" type="integer" value="0" label="Do not predict polymorphic base substitutions that create a homopolymer with this length on each side (with 2 TTATT->TTTTT is rejected)" /> + <param name="strand_coverage" type="integer" value="3" label="Only accept polymorphisms if coverage in each strand is at least this" /> + <param name="bias_pvalue" type="float" value="0.05" label="Only accept polymorphisms if pvalue of strand or read quality bias is greater than this" /> + </when> + <when value="no" /> + </conditional> + + <!-- junction only reference(s) --> + <conditional name="junction_reference"> + <param name="selection" type="select" label="Detect external sequence insertion" help="You can select external sequences to detect insertions"> + <option value="no">Do not detect external sequence insertion</option> + <option value="yes">Detect external sequence insertions</option> + </param> + <when value="yes"> + <repeat name="j_series" title="Junction-only references" min="1"> + <param name="jc_genome" type="data" label="Select an external sequence (fasta or genbank)" /> + </repeat> + </when> + <when value="no" /> + </conditional> + + <!-- Copy Number Evidence --> + <param name="cnv_evidence" type="select" label="Copy number variation prediction (experimental option)" help="Do you want to perform copy number variation prediction"> + <option value="">Do not perform copy number variaion prediction</option> + <option value="--cnv">Perform copy number variation prediction (--cnv)</option> + </param> + + <param name="minqvalue" type="integer" value="3" label="Minimum Phred Q for a base to be considered" /> + + + </inputs> + + <outputs> + <data format="prezip.html" name="outfile" label="Breseq HTML report" /> + </outputs> + + <help> +**Breseq** + +Breseq_ is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes. + +.. _Breseq: http://barricklab.org/twiki/bin/view/Lab/ToolsBacterialGenomeResequencing + +------ + +**Inputs** + +Breseq accepts files in FASTQ format. It does not take pair-end information into account. + +You can either run in clonal (consensus) mode or search for polymorphisms in a population. + +You can also select an external sequence (eg. a transposon) to detect for insertions or horizontal transfer. + + +------ + +**Outputs** + +Breseq outputs a number of files. These are all condensed in a single zipped file. + +It contains output files with the final results, accessible through ``output/index.html`` + +It also contains data files with accessory data, including: + +- ``data/reference.fasta`` (file with reference genome: can be used in eg. IGV browser) +- ``data/reference.gff`` (file with genomic annotations: can be used in eg. IGV browser) +- ``data/areference.bam`` (file with read alignments: can be used in eg. IGV browser) +- ``data/unmatched.*`` (files with read that failed to align: can be used to build an assembly or to eg. blast against NCBI) + + </help> +</tool> +