<tool id="sRNAPipe" name="sRNAPipe" version="1.1.1">
    <description>In-depth study of small RNA</description>
    <macros>
        <xml name="source" token_arg="Argument" token_build="Build argument" token_ref="">
            <conditional name="source">
                <param name="source" type="select" label="Will you select the reference database from your history or use a built-in index?">
                    <option value="indexed">Use a built-in index</option>
                    <option value="history">Use one from the history</option>
                </param>
                <when value="indexed">
                    <param name="indices" argument="@ARG@" type="select" label="Select @REF@">
                        <options from_data_table="bwa_indexes">
                            <filter type="sort_by" column="2" />
                            <validator type="no_options" message="No indexes are available" />
                        </options>
                    </param>
                </when>
                <when value="history">
                    <param name="file" argument="@ARG@" type="data" format="fasta" label="Select @REF@ from history"  help="We will also use @BUILD@"/>
                </when>
            </conditional>
        </xml>
        <xml name="conditional_source" token_arg="Argument" token_build="Build argument" token_ref="" token_name="">
            <conditional name="@NAME@">
                <param name="use_ref" type="select" label="Use @REF@?">
                    <option value="true">Yes</option>
                    <option value="false" selected="true">No</option>
                </param>
                <when value="true">
                    <expand macro="source" arg="@ARG@" build="@BUILD@" ref="@REF@"/>
                </when>
                <when value="false"/>
            </conditional>
        </xml>
    </macros>
    <requirements>
        <requirement type="package" version="1.1.1">srnapipe</requirement>
    </requirements>
    <version_command>srnapipe | grep 'version' | grep "version" | cut -d ' ' -f 3</version_command>
    <command detect_errors="aggressive"><![CDATA[
srnapipe
    #if str($inputs.custom) == 'true'
        #for $x in $inputs.inputs
            --fastq '$x.fastq'
            --fastq_n '$x.fastq_n'
        #end for
    #else
        #for $x in $inputs.fastq
            --fastq '$x'
            --fastq_n '$x.element_identifier'
        #end for
    #end if
    --min $min
    --max $max

    #if $genome.source.source == "history"
    --ref '$genome.source.file'
    --build_index
    #else
    --ref '$genome.source.indices.fields.path'
    #end if
    --mis $genome.mis

    #if $transcripts.source.source == "history"
    --transcripts '$transcripts.source.file'
    --build_transcripts
    #else
    --transcripts '$transcripts.source.indices.fields.path'
    #end if

    #if $te.source.source == "history"
    --TE '$te.source.file'
    --build_TE
    #else
    --TE '$te.source.indices.fields.path'
    #end if
    --misTE $te.misTE

    #if $mirnas.source.source == "history"
    --miRNAs '$mirnas.source.file'
    --build_miRNAs
    #else:
    --miRNAs '$mirnas.source.indices.fields.path'
    #end if

    #if str($snrnas.snrnas.use_ref) == 'true'
        #if str($snrnas.snrnas.source.source) == "history"
    --snRNAs '$snrnas.snrnas.source.file'
    --build_snRNAs
        #else
    --snRNAs '$snrnas.snrnas.source.indices.fields.path'
        #end if
    #end if

    #if str($rrnas.rrnas.use_ref) == 'true'
        #if str($rrnas.rrnas.source.source) == "history"
    --rRNAs '$rrnas.rrnas.source.file'
    --build_rRNAs
        #else
    --rRNAs '$rrnas.rrnas.source.indices.fields.path'
        #end if
    #end if

    #if str($trnas.trnas.use_ref) == 'true'
        #if str($trnas.trnas.source.source) == "history"
    --tRNAs '$trnas.trnas.source.file'
    --build_tRNAs
        #else
    --tRNAs '$trnas.trnas.source.indices.fields.path'
        #end if
    #end if

    --si_min $sirna.si_min
    --si_max $sirna.si_max
    --pi_min $pirna.pi_min
    --pi_max $pirna.pi_max
    --dir $html_out.files_path
    --html $html_out
    --PPPon $PPPon
    --threads '\${GALAXY_SLOTS:-4}'
        ]]>
    </command>
    <inputs>
        <conditional name="inputs">
            <param name="custom" type="select" label="Use custom name for the input sequence files?">
                <option value="true">Yes</option>
                <option value="false" selected="true">No: the names will be extracted automatically</option>
            </param>
            <when value="true">
                <repeat name="inputs" title="Input sequences" min="1">
                    <param argument="--fastq" type="data" format="fastqsanger" label="Input sequences"/>
                    <param argument="--fastq_n" type="text" value="" label="Label for the input sequences"/>
                </repeat>
            </when>
            <when value="false">
                <param argument="--fastq" type="data" format="fastqsanger" multiple="true" label="Input sequences" help="Also set a name with --fastq_n"/>
            </when>
        </conditional>
        <param argument="--min" type="integer" value="18" label="Minimum read size"/>
        <param argument="--max" type="integer" value="29" label="Maximum read size"/>
        <section name="genome" title="Reference genome" expanded="true">
            <expand macro="source" arg="--ref" build="--build_index" ref="a reference genome"/>
            <param argument="--mis" type="integer" value="0" label="Maximal genome mismatches"/>
        </section>
        <section name="transcripts" title="Transcripts" expanded="true">
            <expand macro="source" arg="--transcripts" build="--build_transcripts" ref="reference transcript sequences"/>
        </section>
        <section name="te" title="Transposable Elements" expanded="true">
            <expand macro="source" arg="--TE" build="--build_TE" ref="reference TE sequences"/>
            <param argument="--misTE" type="integer" value="3" label="maximal TE mismatches"/>
        </section>
        <section name="mirnas" title="miRNAs" expanded="true">
            <expand macro="source" arg="--miRNAs" build="--build_miRNAs" ref="reference miRNAs sequences"/>
        </section>
        <section name="snrnas" title="snRNAs" expanded="true">
            <expand macro="conditional_source" name="snrnas" arg="--snRNAs" build="--build_snRNAs" ref="reference snRNAs sequences"/>
        </section>
        <section name="rrnas" title="rRNAs" expanded="true">
            <expand macro="conditional_source" name="rrnas" arg="--rRNAs" build="--build_rRNAs" ref="reference rRNAs sequences"/>
        </section>
        <section name="trnas" title="tRNAs" expanded="true">
            <expand macro="conditional_source" name="trnas" arg="--tRNAs" build="--build_tRNAs" ref="reference tRNAs sequences"/>
        </section>
        <section name="sirna" title="siRNA" expanded="true">
            <param argument="--si_min" type="integer" value="21" label="Lower bound for siRNA range"/>
            <param argument="--si_max" type="integer" value="21" label="Higher bound of siRNA range"/>
        </section>
        <section name="pirna" title="piRNA" expanded="true">
            <param argument="--pi_min" type="integer" value="23" label="lower bound of piRNA range"/>
            <param argument="--pi_max" type="integer" value="29" label="higher bound of piRNA range"/>
        </section>
        <param name="PPPon" argument="--PPPon" type="boolean" truevalue="true" falsevalue="false" checked="true" label="PPPartners"/>
    </inputs>
    <outputs>
        <data format="html" name="html_out" label="${tool.name} on ${on_string}: HTML report"/>
        <collection type="list" label="${tool.name} on ${on_string}: FastQ outputs" name="output_fastqsanger">
            <discover_datasets format ="fastqsanger" pattern="__designation_and_ext__" directory="fastq_dir" />
        </collection>
    </outputs>
    <tests>
        <test>
            <conditional name="inputs">
                <param name="custom" value="false"/>
                <param name="fastq" value="reads-sample-small.fastq"/>
            </conditional>
            <param name="min" value="18" />
            <param name="max" value="29" />
            <section name="genome">
                <conditional name="source">
                    <param name="source" value="history" />
                    <param name="file" value ="genome-small.fa" />
                </conditional>
                <param name="mis" value="0" />
            </section>
            <section name="transcripts">
                <conditional name="source">
                    <param name="source" value="history" />
                    <param name="file" value ="transcripts-file-small.fa" />
                </conditional>
            </section>
            <section name="te">
                <conditional name="source">
                    <param name="source" value="history" />
                    <param name="file" value ="TE-file-small.fa" />
                </conditional>
                <param name="misTE" value="3" />
            </section>
            <section name="mirnas">
                <conditional name="source">
                    <param name="source" value="history" />
                    <param name="file" value ="mirbase-21-dme-hairpins-16jul2015.fa" />
                </conditional>
            </section>
            <section name="snrnas">
                <conditional name="snrnas">
                    <param name="use_ref" value="true"/>
                    <conditional name="source">
                        <param name="source" value="history" />
                        <param name="file" value ="dmel-all-sn-snoRNA-r6.03.fasta" />
                    </conditional>
                </conditional>
            </section>
            <section name="rrnas">
                <conditional name="rrnas">
                    <param name="use_ref" value="true"/>
                    <conditional name="source">
                        <param name="source" value="history" />
                        <param name="file" value ="dmel-all-rRNA-r6.03.fasta" />
                    </conditional>
                </conditional>
            </section>
            <section name="trnas">
                <conditional name="trnas">
                    <param name="use_ref" value="true"/>
                    <conditional name="source">
                        <param name="source" value="history" />
                        <param name="file" value ="dmel-all-tRNA-r6.03.fasta" />
                    </conditional>
                </conditional>
            </section>
            <section name="sirna">
                <param name="si_min" value="21" />
                <param name="si_max" value="21" />
            </section>
            <section name="pirna">
                <param name="pi_min" value="23" />
                <param name="pi_max" value="29" />
            </section>
            <param name="PPPon" value="true" />
            <output name='html_out' file="res.html" compare='diff' lines_diff = '10'/>
            <output_collection name="output_fastqsanger" type="list">
                <element name="reads-sample-small.fastq_all_mappers" file="fastq_dir/reads-sample-small.fastq_all_mappers.fastq" />
                <element name="reads-sample-small.fastq-bonafide_reads-genome" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-genome.fastq" />
                <element name="reads-sample-small.fastq-bonafide_reads-genome_uni" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-genome_uni.fastq" />
                <element name="reads-sample-small.fastq-bonafide_reads-TEs" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs.fastq" />
                <element name="reads-sample-small.fastq-bonafide_reads-TEs_uni" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs_uni.fastq" />
                <element name="reads-sample-small.fastq-bonafide_reads-transcripts" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts.fastq" />
                <element name="reads-sample-small.fastq-bonafide_reads-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts_uni.fastq" />
                <element name="reads-sample-small.fastq-miRNAs-genome" file="fastq_dir/reads-sample-small.fastq-miRNAs-genome.fastq" />
                <element name="reads-sample-small.fastq-miRNAs-genome_uni" file="fastq_dir/reads-sample-small.fastq-miRNAs-genome_uni.fastq" />
                <element name="reads-sample-small.fastq-miRNAs-TEs_uni" file="fastq_dir/reads-sample-small.fastq-miRNAs-TEs_uni.fastq" />
                <element name="reads-sample-small.fastq-miRNAs-transcripts" file="fastq_dir/reads-sample-small.fastq-miRNAs-transcripts.fastq" />
                <element name="reads-sample-small.fastq-miRNAs-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-miRNAs-transcripts_uni.fastq" />
                <element name="reads-sample-small.fastq-piRNAs-genome" file="fastq_dir/reads-sample-small.fastq-piRNAs-genome.fastq" />
                <element name="reads-sample-small.fastq-piRNAs-genome_uni" file="fastq_dir/reads-sample-small.fastq-piRNAs-genome_uni.fastq" />
                <element name="reads-sample-small.fastq-piRNAs-TEs" file="fastq_dir/reads-sample-small.fastq-piRNAs-TEs.fastq" />
                <element name="reads-sample-small.fastq-piRNAs-TEs_uni" file="fastq_dir/reads-sample-small.fastq-piRNAs-TEs_uni.fastq" />
                <element name="reads-sample-small.fastq-piRNAs-transcripts" file="fastq_dir/reads-sample-small.fastq-piRNAs-transcripts.fastq" />
                <element name="reads-sample-small.fastq-piRNAs-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-piRNAs-transcripts_uni.fastq" />
                <element name="reads-sample-small.fastq-siRNAs-genome" file="fastq_dir/reads-sample-small.fastq-siRNAs-genome.fastq" />
                <element name="reads-sample-small.fastq-siRNAs-genome_uni" file="fastq_dir/reads-sample-small.fastq-siRNAs-genome_uni.fastq" />
                <element name="reads-sample-small.fastq-siRNAs-TEs" file="fastq_dir/reads-sample-small.fastq-siRNAs-TEs.fastq" />
                <element name="reads-sample-small.fastq-siRNAs-TEs_uni" file="fastq_dir/reads-sample-small.fastq-siRNAs-TEs_uni.fastq" />
                <element name="reads-sample-small.fastq-siRNAs-transcripts" file="fastq_dir/reads-sample-small.fastq-siRNAs-transcripts.fastq" />
                <element name="reads-sample-small.fastq-siRNAs-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-siRNAs-transcripts_uni.fastq" />
                <element name="reads-sample-small.fastq_unique_mappers" file="fastq_dir/reads-sample-small.fastq_unique_mappers.fastq" />
                <element name="reads-sample-small.fastq_unmapped" file="fastq_dir/reads-sample-small.fastq_unmapped.fastq" />
            </output_collection>
        </test>
    </tests>
    <help>
 	**User manual**
 	"https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf"
    </help>
    <citations>
        <citation type="doi">10.1186/s13100-018-0130-7</citation>
    </citations>
</tool>