comparison breseq.xml @ 10:e21c4ceb0039 draft default tip

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<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>