<tool id="samtools_cram_to_bam" name="samtools CRAM to BAM" version="@TOOL_VERSION@+galaxy1">
    <description>convert CRAM alignments to BAM format</description>

    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>

    <command><![CDATA[
        #set input_cram = "input.cram"
        ln -s '${input_alignment}' '${input_cram}' &&
        #if str( $input_alignment.metadata.cram_index ) != "None":
            ln -f -s '${input_alignment.metadata.cram_index}' '${input_cram}.crai' &&
        #end if

        #if $reference_source.reference_source_selector == 'history':
            #set ref_fa = 'ref.fa'
            ln -s '${reference_source.input_reference}' ref.fa &&
        #else:
            #set ref_fa = str( $reference_source.input_reference.fields.path )
        #end if

        samtools view
            #if $parameter_regions.target_region == "regions_bed_file"
                -L '${parameter_regions.regions_bed_file}'
            #end if
            -@ \${GALAXY_SLOTS:-2}
            -b
            -T '$ref_fa'
            -o '$output_alignment'
            '$input_cram'
            #if $parameter_regions.target_region == "region"
                '${parameter_regions.region_string}'
            #end if
    ]]></command>

    <inputs>
        <param name="input_alignment" type="data" format="cram" label="CRAM alignment file"/>
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Load reference genome from">
                <option value="cached">Local cache</option>
                <option value="history">History</option>
            </param>
            <when value="cached">
                <param name="input_reference" type="select" label="Reference genome">
                    <options from_data_table="fasta_indexes">
                        <filter type="data_meta" ref="input_alignment" key="dbkey" column="dbkey" />
                    </options>
                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                </param>
            </when>
            <when value="history">
                <param name="input_reference" type="data" format="fasta" label="Reference FASTA file"/>
            </when>
        </conditional>
        <conditional name="parameter_regions">
            <param name="target_region" type="select" label="Choose conversion within specific genomic region(s)">
                <option value="entire_input_file">Entire BAM alignment file</option>
                <option value="region">Specific region</option>
                <option value="regions_bed_file">List of specific regions (BED file)</option>
            </param>
            <when value="entire_input_file" />
            <when value="region">
                <param name="region_string" type="text" label="Samtools: region in which pileup is generated" help="e.g. chrX or chr:start-end" />
            </when>
            <when value="regions_bed_file">
                <param name="regions_bed_file" argument="-L" type="data" format="bed" label="Only include reads overlapping this BED file" />
            </when>
        </conditional>
    </inputs>

    <outputs>
        <data name="output_alignment" format="bam" label="$tool.name on ${on_string}.bam"></data>
    </outputs>

    <tests>
        <test>
            <param name="input_alignment" value="test.cram" ftype="cram" />
            <param name="reference_source_selector" value="history" />
            <param name="input_reference" value="test.fa" />

            <output name="output_alignment" file="test.bam" compare="sim_size" delta="250" />
        </test>
        <test>
            <param name="input_alignment" value="test.cram" ftype="cram" />
            <param name="reference_source_selector" value="history" />
            <param name="input_reference" value="test.fa" />
            <param name="target_region" value="region" />
            <param name="region_string" value="CHROMOSOME_I" />

            <output name="output_alignment" file="test.bam" compare="sim_size" delta="250" />
        </test>
        <test>
            <param name="input_alignment" value="test.cram" ftype="cram" />
            <param name="reference_source_selector" value="history" />
            <param name="input_reference" value="test.fa" />
            <param name="target_region" value="regions_bed_file" />
            <param name="regions_bed_file" value="test.bed" ftype="bed" />

            <output name="output_alignment" file="test.bam" compare="sim_size" delta="250" />
        </test>
        <test>
            <param name="input_alignment" value="test2.cram" dbkey="equCab2" ftype="cram" />
            <param name="reference_source_selector" value="cached" />
            <param name="input_reference" value="equCab2chrM" />
            <param name="target_region" value="entire_input_file" />
            <output name="output_alignment" file="sam_to_bam_out2.bam" compare="sim_size" delta="250" />
        </test>
    </tests>

    <help><![CDATA[
**What this tool does**

Converts alignments from the CRAM format to the BAM format using the ``samtools view`` command.
    ]]></help>
    <expand macro="citations"/>
</tool>