<tool id="gstf_preparation" name="GeneSeqToFamily preparation" version="0.4.1">
    <description>converts data for the workflow</description>
    <command detect_errors="exit_code">
<![CDATA[
python '$__tool_directory__/gstf_preparation.py'
#for $q in $queries
    --gff3 '${q.genome}:${q.gff3_input}'
#end for
#if str($json) != 'None'
    #for $v in $json
        --json '$v'
    #end for
#end if
#for $fasta_input in $fasta_inputs
    --fasta '${fasta_input}'
#end for
#if $headers
    --headers
#end if
#if $longestCDS
    -l
#end if
#if $regions
    --regions '$regions'
#end if
-o '$output_db'
--of '$output_fasta'
--ff '$filtered_fasta'
]]>
    </command>

    <inputs>
        <repeat name="queries" title="GFF3 dataset">
            <param name="gff3_input" type="data" format="gff3" label="GFF3 dataset" />
            <param name="genome" type="text" label="Genome name" help="Genome name without whitespaces or special characters">
                <validator type="empty_field" />
            </param>
        </repeat>
        <param name="json" type="data" format="json" multiple="true" optional="true" label="Gene features in JSON format generated by 'Get features by Ensembl ID' tool" />
        <param name="fasta_inputs" type="data" format="fasta" multiple="true" label="Corresponding CDS datasets in FASTA format" help="Each FASTA header line should start with a transcript id" />
        <param name="longestCDS" type="boolean" checked="false" label="Keep only the longest CDS per gene" />
        <param name="headers" type="boolean" checked="true" label="Change the header line of the FASTA sequences to the &gt;TranscriptId_species format" help="As required by TreeBest, part of the GeneSeqToFamily workflow" />
        <param name="regions" type="text" optional="true" label="Comma-separated list of region IDs (e.g. chromosomes or scaffolds) for which FASTA sequences should be filtered" help="Region IDs are in the `seqid` column for GFF3 and in the `seq_region_name` field in JSON. This is typically used to filter chromosomes with a non-standard genetic code, like mitochondria, to be analysed separately" />
    </inputs>

    <outputs>
         <data name="output_db" format="sqlite" label="${tool.name} on ${on_string}: SQLite" />
         <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string}: FASTA" />
         <data name="filtered_fasta" format="fasta" label="${tool.name} on ${on_string}: filtered sequences" />
    </outputs>

    <tests>
        <test>
            <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
            <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3" />
            <param name="genome" value="caenorhabditis_elegans" />
            <param name="longestCDS" value="false" />
            <param name="headers" value="true" />

            <output name="output_db" file="test1.sqlite" compare="sim_size" />
            <output name="output_fasta" file="test1.fasta" />
            <output name="filtered_fasta" file="test1.ns.fasta" />
        </test>
        <test>
            <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
            <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3" />
            <param name="genome" value="caenorhabditis_elegans" />
            <param name="longestCDS" value="true" />
            <param name="headers" value="true" />

            <output name="output_db" file="test1.sqlite" compare="sim_size" />
            <output name="output_fasta" file="test1_longest.fasta" />
            <output name="filtered_fasta" file="test1.ns.fasta" />
        </test>
        <test>
            <param name="fasta_inputs" ftype="fasta" value="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
            <param name="gff3_input" ftype="gff3" value="Caenorhabditis_elegans.WBcel235.87.chromosome.I.shortened.gff3" />
            <param name="genome" value="caenorhabditis_elegans" />
            <param name="longestCDS" value="false" />
            <param name="headers" value="false" />

            <output name="output_db" file="test1.sqlite" compare="sim_size" />
            <output name="output_fasta" file="Caenorhabditis_elegans.WBcel235.cds.all.shortened.fa" />
            <output name="filtered_fasta" file="test1.ns.fasta" />
        </test>
        <test>
            <param name="fasta_inputs" ftype="fasta" value="CDS.fasta" />
            <param name="json" ftype="json" value="gene.json" />
            <param name="longestCDS" value="false" />
            <param name="headers" value="true" />

            <output name="output_db" file="test4.sqlite" compare="sim_size" />
            <output name="output_fasta" file="test4.fasta" />
            <output name="filtered_fasta" file="test4.ns.fasta" />
        </test>
        <test>
            <param name="fasta_inputs" ftype="fasta" value="CDS.fasta" />
            <param name="json" ftype="json" value="gene.json" />
            <param name="longestCDS" value="false" />
            <param name="headers" value="true" />
            <param name="regions" value="X" />

            <output name="output_db" file="test5.sqlite" compare="sim_size" />
            <output name="output_fasta" file="test5_filtered.fasta" />
            <output name="filtered_fasta" file="test5.ns.fasta" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

This tool converts a set of GFF3 and/or JSON gene feature information datasets into SQLite format.

It also filters the CDS FASTA datasets to:

- remove coding sequences whose length is not a multiple of 3
- keep only the transcripts present in the gene feature information.

Optionally it can also keep only the longest CDS per gene and/or change the header line of the FASTA sequences to the >TranscriptId_species format (as required by TreeBest, part of the GeneSeqToFamily workflow).

Example GFF3 file::

    scaffold_0  MYZPE13164_Clone_G006_v1.0  gene            44968   69413   .   -   .   ID=MYZPE13164_G006_v1.0_000000030;Name=MYZPE13164_G006_v1.0_000000030;biotype=protein_coding
    scaffold_0  MYZPE13164_Clone_G006_v1.0  mRNA            44968   69413   .   -   .   ID=MYZPE13164_G006_v1.0_000000030.1;Parent=MYZPE13164_G006_v1.0_000000030;Name=MYZPE13164_G006_v1.0_000000030.1;biotype=protein_coding;_AED=0.31
    scaffold_0  MYZPE13164_Clone_G006_v1.0  three_prime_utr 44968   46637   .   -   .   ID=MYZPE13164_G006_v1.0_000000030.1.3utr1;Parent=MYZPE13164_G006_v1.0_000000030.1
    scaffold_0  MYZPE13164_Clone_G006_v1.0  exon            44968   47432   .   -   .   ID=MYZPE13164_G006_v1.0_000000030.1.exon1;Parent=MYZPE13164_G006_v1.0_000000030.1
    scaffold_0  MYZPE13164_Clone_G006_v1.0  CDS             46638   47432   .   -   0   ID=MYZPE13164_G006_v1.0_000000030.1.cds1;Parent=MYZPE13164_G006_v1.0_000000030.1
    scaffold_0  MYZPE13164_Clone_G006_v1.0  exon            53325   53539   .   -   .   ID=MYZPE13164_G006_v1.0_000000030.1.exon2;Parent=MYZPE13164_G006_v1.0_000000030.1
    scaffold_0  MYZPE13164_Clone_G006_v1.0  CDS             53325   53539   .   -   2   ID=MYZPE13164_G006_v1.0_000000030.1.cds2;Parent=MYZPE13164_G006_v1.0_000000030.1
    scaffold_0  MYZPE13164_Clone_G006_v1.0  exon            54614   54719   .   -   .   ID=MYZPE13164_G006_v1.0_000000030.1.exon3;Parent=MYZPE13164_G006_v1.0_000000030.1
    scaffold_0  MYZPE13164_Clone_G006_v1.0  CDS             54614   54719   .   -   0   ID=MYZPE13164_G006_v1.0_000000030.1.cds3;Parent=MYZPE13164_G006_v1.0_000000030.1
    scaffold_0  MYZPE13164_Clone_G006_v1.0  CDS             54852   55106   .   -   0   ID=MYZPE13164_G006_v1.0_000000030.1.cds4;Parent=MYZPE13164_G006_v1.0_000000030.1
    scaffold_0  MYZPE13164_Clone_G006_v1.0  exon            54852   55117   .   -   .   ID=MYZPE13164_G006_v1.0_000000030.1.exon4;Parent=MYZPE13164_G006_v1.0_000000030.1
    scaffold_0  MYZPE13164_Clone_G006_v1.0  five_prime_utr  55107   55117   .   -   .   ID=MYZPE13164_G006_v1.0_000000030.1.5utr1;Parent=MYZPE13164_G006_v1.0_000000030.1
    scaffold_0  MYZPE13164_Clone_G006_v1.0  five_prime_utr  68851   69413   .   -   .   ID=MYZPE13164_G006_v1.0_000000030.1.5utr2;Parent=MYZPE13164_G006_v1.0_000000030.1
    scaffold_0  MYZPE13164_Clone_G006_v1.0  exon            68851   69413   .   -   .   ID=MYZPE13164_G006_v1.0_000000030.1.exon5;Parent=MYZPE13164_G006_v1.0_000000030.1

The following features are parsed: **gene**, **mRNA**, **transcript**, **exon**, **five_prime_utr**, **three_prime_utr** and **CDS**, all other are ignored. Also, **ID** and **Parent** attributes in the 9th column are needed to create relations among features.

.. class:: warningmark

If a value in the **ID** and **Parent** attribute contains a colon, everything up to the first colon will be discarded.
]]>
    </help>
    <citations>
    </citations>
</tool>