<?xml version="1.0"?>
<tool id="bamtools" name="Convert, Merge, Randomize" version="2.4.0">
    <description>BAM datasets and perform other transformations</description>
    <requirements>
        <requirement type="package" version="2.4.0">bamtools</requirement>
        <requirement type="package" version="1.3.1">samtools</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command>
        <![CDATA[
            ##set up input files
            #for $bam_count, $input_bam in enumerate( $input_bams ):
                ln -s "${input_bam}" "localbam_${bam_count}.bam" &&
                ln -s "${input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &&
            #end for
            #if str( $analysis_type.analysis_type_selector ) == "convert":
                #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
                    #set $reference_fasta_filename = "localref.fa"
                    #if str( $analysis_type.format_type.reference_source.reference_source_selector ) == "history":
                        ln -s "${analysis_type.format_type.reference_source.ref_file}" "${reference_fasta_filename}" &&
                        samtools faidx "${reference_fasta_filename}" 2>&1 || echo "Error running samtools faidx for bamtools convert" >&2 &&
                    #else:
                        #set $reference_fasta_filename = str( $analysis_type.format_type.reference_source.ref_file.fields.path )
                    #end if
                #end if
            #end if
            bamtools
            #if str( $analysis_type.analysis_type_selector ) == "convert":
                convert
                -format ${analysis_type.format_type.format_type_selector}
                #if str( $analysis_type.format_type.format_type_selector ) == "pileup":
                    ${analysis_type.format_type.mapqual}
                    -fasta "${reference_fasta_filename}"
                #elif str( $analysis_type.format_type.format_type_selector ) == "sam":
                    ${analysis_type.format_type.noheader}
                #end if
                -out $out_file1
            #elif str( $analysis_type.analysis_type_selector ) == "count":
                count
                > $out_file1
            #elif str( $analysis_type.analysis_type_selector ) == "coverage":
                coverage
                -out $out_file1
            #elif str( $analysis_type.analysis_type_selector ) == "header":
                header
                > $out_file1
            #elif str( $analysis_type.analysis_type_selector ) == "merge":
                merge
                -out $out_file1
            #elif str( $analysis_type.analysis_type_selector ) == "random":
                random
                -n ${analysis_type.count}
                -seed ${analysis_type.seed}
                -out $out_file1
            #elif str( $analysis_type.analysis_type_selector ) == "revert":
                revert
                ${analysis_type.keepDuplicate}
                ${analysis_type.keepQualities}
                -out $out_file1
            #elif str( $analysis_type.analysis_type_selector ) == "sort":
                sort
                ${analysis_type.byname}
                -out $out_file1
            #end if
            #for $bam_count, $input_bam in enumerate( $input_bams ):
                -in "localbam_${bam_count}.bam"
            #end for
        ]]>
    </command>
    <inputs>
        <param name="input_bams" type="data" format="bam" label="BAM dataset(s) to filter" min="1" multiple="True"/>
        <conditional name="analysis_type">
            <param name="analysis_type_selector" type="select" label="Select BAM manipulation" help="See help below for detailed description of each tool">
                <option value="convert">Convert</option>
                <option value="count">Count</option>
                <option value="coverage">Coverage</option>
                <option value="header">Header</option>
                <option value="merge">Merge</option>
                <option value="random">Random</option>
                <option value="revert">Revert</option>
                <!-- The sort option below is commented out as BAM files in Galaxy are reference sorted by dafault. -->
                <!-- Allowing users for sort files may break donstream functionality. -->
                <!-- To enable sort option simply uncomment the line below: -->
                <!--  <option value="sort">Sort</option> -->
            </param>
            <when value="convert">
                <conditional name="format_type">
                    <param name="format_type_selector" type="select" help="Select what to convert your BAM to">
                        <option value="bed">BED</option>
                        <option value="fasta">FASTA</option>
                        <option value="fastq">FASTQ</option>
                        <option value="json">JSON</option>
                        <option value="pileup">Pileup</option>
                        <option value="sam">SAM</option>
                        <option value="yaml">YAML</option>
                    </param>
                    <when value="bed"/>
                    <when value="fasta"/>
                    <when value="fastq"/>
                    <when value="json"/>
                    <when value="yaml"/>
                    <when value="pileup">
                        <conditional name="reference_source">
                            <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
                                <option value="cached">Locally cached</option>
                                <option value="history">History</option>
                            </param>
                            <when value="cached">
                                <param name="ref_file" type="select" label="Using reference genome">
                                    <options from_data_table="sam_fa_indexes">
                                        <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
                                    </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"> <!-- FIX ME!!!! -->
                                <param name="ref_file" type="data" format="fasta" label="Using reference file" />
                            </when>
                        </conditional>
                        <param name="mapqual" type="boolean" truevalue="-mapqual" falsevalue="" label="Print quality scores?" />
                    </when>
                    <when value="sam">
                        <param name="noheader" type="boolean" truevalue="-noheader" falsevalue="" label="Do not print header" />
                    </when>
                </conditional>
            </when>
            <when value="count" />
            <when value="coverage" />
            <when value="header" />
            <when value="merge" />
            <when value="random">
                <param name="count" type="integer" value="10000" label="Number of random alignments to grab" help="No duplicate checking is perfomed" />
                <param name="seed" type="integer" value="1024" label="Random number generator seed" help="Use the same seed for reproducible results" />
            </when>
            <when value="revert">
                <param name="keepDuplicate" type="boolean" truevalue="-keepDuplicate" falsevalue="" label="Keep duplicates marked" help="Do not remove duplicate marks" />
                <param name="keepQualities" type="boolean" truevalue="-keepQualities" falsevalue="" label="Keep base qualities" help="Do not replace qualities with contect of OQ tag" />
            </when>
            <!--
            <when value="sort">
                <param name="byname" type="boolean" truevalue="-byname" falsevalue="" label="Sort by name" help="Checked: sort by name; Unchecked: sort by coordinate"/>
            </when>
            -->
        </conditional>
    </inputs>
    <outputs>
        <data format="txt" name="out_file1">
            <change_format>
                <when input="analysis_type.format_type.format_type_selector" value="bed" format="bed" />
                <when input="analysis_type.format_type.format_type_selector" value="fasta" format="fasta" />
                <when input="analysis_type.format_type.format_type_selector" value="fastq" format="fastq" />
                <when input="analysis_type.format_type.format_type_selector" value="sam" format="sam" />
                <when input="analysis_type.format_type.format_type_selector" value="pileup" format="pileup" />
                <when input="analysis_type.analysis_type_selector" value="coverage" format="tabular" />
                <when input="analysis_type.analysis_type_selector" value="merge" format="bam" />
                <when input="analysis_type.analysis_type_selector" value="random" format="bam" />
                <when input="analysis_type.analysis_type_selector" value="revert" format="bam" />
                <when input="analysis_type.analysis_type_selector" value="sort" format="bam" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
            <param name="analysis_type_selector" value="convert"/>
            <param name="format_type_selector" value="pileup"/>
            <param name="reference_source_selector" value="history" />
            <param name="mapqual" value="true" />
            <param name="ref_file" ftype="fasta" value="bamtools-fasta.fa"/>
            <output name="output_bam" file="bamtools-convert-pileup.pu" />
        </test>
        <test>
            <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
            <param name="analysis_type_selector" value="count"/>
            <output name="output_bam" file="bamtools-count.tab" />
        </test>
        <test>
            <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
            <param name="analysis_type_selector" value="coverage"/>
            <output name="output_bam" file="bamtools-coverage.tab" />
        </test>
        <test>
            <param name="input_bams" ftype="bam" value="bamtools-input1.bam"/>
            <param name="analysis_type_selector" value="header"/>
            <output name="output_bam" file="bamtools-header.txt" />
        </test>
    </tests>
    <help>

**What is does**

BAMTools is a collection of utilities for manipulation on BAM files. It is based on BAMtools suite of tools by Derek Barnett (https://github.com/pezmaster31/bamtools).
This Galaxy implementation of BAMTools utilities includes seven utilities - Convert, Count, Coverage, Header, Merge, Random, and Revert - decsribed in detail below.

-----

**Convert**

Converts BAM dataset(s) into BED, FASTA, FASTQ, JSON, Pileup, SAM, or YAML formats. Note that the conversion to the pileup format requires providing a reference sequence either
cashed at this Galaxy instance, or provided by you as a FASTA dataset from History.

-----

**Count**

Counts a number of alignments in a BAM dataset(s).

-----

**Coverage**

Prints per-base coverage for a BAM dataset.

-----

**Header**

Prints header from a BAM dataset(s).

------

**Merge**

Merges multiple BAM datasets into a single one. Obviously, you need to select multiple BAMs as input, which is done by pressing the "**Add new BAM dataset(s) to filter**" button.

------

**Random**

Grabs a specified number of random lines from BAM dataset(s).

------

**Revert**

Removes duplicate marks and restores original (non-recalibrated) base qualities.

-----

.. class:: infomark

**More information**

Additional information about BAMtools can be found at https://github.com/pezmaster31/bamtools/wiki

    </help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btr174</citation>
    </citations>
</tool>