<tool id="index_ref" name="0. Get or Build Index" version="1.0.1" profile="16.10">
    <description>by lookup from BioProject or from an assembly</description>
    <requirements>
        <requirement type="package" version="2.3.4">bowtie2</requirement>
        <requirement type="package" version="1.6">samtools</requirement>
        <requirement type="package" version="1.5.11">boto3</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if $source.source_select == 'bioproject'
            ${__tool_directory__}/snp-cache.py snp_bioproject_references "${bioproject}" -o ${output}   &&
            ${__tool_directory__}/snp-cache.py snp_bioproject_indexes "${bioproject}" -o ${faidx}
        #else
        mkdir ./reference                                       &&
        cp ${input} ./reference/reference.fasta                 &&
        export ID=\$(md5sum $input | cut -c -32)                &&
        ${__tool_directory__}/snp-cache.py snp_local_references \$ID
                -c "
                    bowtie2-build ./reference/reference.fasta --quiet --threads \${GALAXY_SLOTS:-4} ./reference/reference &&
                    tar -zcf /dev/stdout ./reference/ref*bt2
                    "
                -o ${output}
                -l $cache_log
        
        ##&& ${__tool_directory__}/snp-cache.py snp_local_indexes \$ID
        ##        -c "
        ##            samtools faidx ./reference/reference.fasta && cat ./reference/reference.fasta.fai
        ##        "
        ##        -o ${faidx}
        #end if
        && cat $cache_log
    ]]></command>
    <inputs>
    	<conditional name="source">
            <param name="source_select" type="select" label="Use the reference associated with a provided BioProject, a curated GalaxyTrakr reference, or a reference from your history">
                <option value="bioproject">Provide a BioProject</option>
                <option value="curated">Use a GalaxyTrakr reference</option>
                <option value="history">Use a reference from your history</option>
            </param>
            <when value="bioproject">
                <param type="data" name="bioproject" format="text"/>
            </when>
            <when value="curated">
    			<param name="input" type="select" label="Select reference fasta">
    				<options from_data_table="all_fasta">
    				    <filter type="sort_by" column="2"/>
        				<validator type="no_options" message="No assemblies are available for the selected input dataset"/>
    				</options>
    			</param>
    		</when>
            <when value="history">
                <param type="data" name="input" format="fasta" label="Select reference FASTA"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data label="Indexed reference (bt2)" name="output" format="tar" />
        <!-- <data label="Indexed reference (faidx)" name="faidx" format="fai" /> -->
        <data label="S3 Cache log" name="cache_log" format="txt" hidden="true" />
    </outputs>
    <tests>
        <test>
            <param name="source_select" value="history" />
            <param name="input" value="reference/lambda_virus.fasta" />
            <output name="output" value="reference/reference.tar.gz" decompress="true" lines_diff="10" />
            <!-- <output name="faidx" value="reference/reference.fasta.fai" /> -->
        </test>
    </tests>
    <help><![CDATA[
        <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>
    ]]></help>
    <citations>
        <citation type="doi">10.7717/peerj-cs.20</citation>
<!--        <citation type="bibtex">
@misc{cfsan-snp-pipeline,
  author = {Steve Davis and James Pettengill and Yan Luo and Justin Payne and Albert Shpuntoff and Rugh Rand and Errol Strain},
  year = {2015},
  title = {CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data},
  url = {https://doi.org/10.7717/peerj-cs.20},
  journal = {PeerJ Computer Science},
}</citation> -->
    </citations>
</tool>