<tool id="fgbio_fastq_to_bam" name="fgbio FastqToBam" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
    <description>Generates an unmapped BAM file from fastq files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <version_command>fgbio --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        fgbio FastqToBam 
        --input 
        #for $input in $inputs
            '$input'
        #end for
        --sample='$sample'
        --library='$library'
        #if $read_structures:
            --read-structures $read_structures
        #end if
        --sort='$sort'
        --output '$output'
        ## optional bam header content
        #if $bam_header.umi_tag
            --umi-tag='$bam_header.umi_tag'
        #end if
        #if $bam_header.predicted_insert_size
            --predicted-insert-size='$bam_header.predicted_insert_size'
        #end if
        #if $bam_header.read_group
            --read-group='$bam_header.read_group'
        #end if
        #if $bam_header.description
            --description='$bam_header.description'
        #end if
        #if $bam_header.platform
            --platform='$bam_header.platform'
        #end if
        #if $bam_header.platform_model
            --platform-model='$bam_header.platform_model'
        #end if
        #if $bam_header.platform_model
            --platform-model='$bam_header.platform_model'
        #end if
        #if $bam_header.platform_unit
            --platform-unit='$bam_header.platform_unit'
        #end if
        #if $bam_header.sequencing_center
            --sequencing-center='$bam_header.sequencing_center'
        #end if
        #if $bam_header.comment
            --comment='$bam_header.comment'
        #end if
    ]]></command>
    <inputs>
        <param name="inputs" type="data" format="fastq" multiple="true" label="Fastq files corresponding to each sequencing read"/>
        <param argument="--sample" type="text" value="" label="The name of the sequenced sample">
        </param>
        <param argument="--library" type="text" value="" label="The name/ID of the sequenced library">
        </param>
        <param argument="--read-structures" type="text" value="" optional="true" label="Read structures, one for each of the FASTQ">
            <expand macro="read_structures_validator" />
        </param>
        <param argument="--sort" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Sort bam by queryname" 
               help="If true, queryname sort the BAM file, otherwise preserve input order."/>
        <section name="bam_header" title="BAM Header" expanded="false">
            <param argument="--umi-tag" type="text" value="" optional="true" label="Tag in which to store molecular barcodes/UMIs" help="Default: RX"> 
                <expand macro="sam_tag_validator" />
            </param>
            <param argument="--predicted-insert-size" type="integer" value="" optional="true" label="Predicted median insert size, to insert into the read group header"/> 
            <param argument="--read-group" type="text" value="" optional="true" label="Read group ID to use in the file header" help="Default: A"/> 
            <param argument="--description" type="text" value="" optional="true" label="Description of the read group"/> 
            <param argument="--platform" type="text" value="" optional="true" label="Sequencing Platform" help="Default: illumina"/> 
            <param argument="--platform-model" type="text" value="" optional="true" label="Platform model to insert into the group header (ex. miseq, hiseq2500, hiseqX)"/> 
            <param argument="--platform-unit" type="text" value="" optional="true" label="Platform unit (e.g. 'flowcell-barcode.lane.sample-barcode')"/> 
            <param argument="--sequencing-center" type="text" value="" optional="true" label="The sequencing center from which the data originated"/> 
            <param argument="--comment" type="text" value="" optional="true" label="Comment to include in the output header"/> 
        </section>
    </inputs>
    <outputs>
        <data name="output" format="unsorted.bam" />
    </outputs>
    <help><![CDATA[
**fgbio FastqToBam**

Generates an unmapped BAM (or SAM or CRAM) file from fastq files. Takes in one or more fastq files (optionally gzipped), each representing a different sequencing read (e.g. R1, R2, I1 or I2) and can use a set of read structures to allocate bases in those reads to template reads, sample indices, unique molecular indices, or to designate bases to be skipped over.

@READ_STRUCTURES_HELP@

http://fulcrumgenomics.github.io/fgbio/tools/latest/FastqToBam.html
    ]]></help>
    <expand macro="citations" />
</tool>