<tool id="ensembl_variant_report" name="Ensembl Variant Report" version="0.2.0">
    <requirements>
        <requirement type="package" version="1.40">gtf_to_genes</requirement>
        <requirement type="package" version="3.1.4">twobitreader</requirement>
        <requirement type="package" version="1.62">biopython</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
         python '$__tool_directory__/ensembl_variant_report.py'
         #if $ref.ref_source == 'cached':
             --twobit="$ref.ref_loc.fields.path"
         #else
             --twobit="$ref.ref_file"
         #end if
         --gene_model="$gtf_file"
         #if $variant.fmt == 'vcf':
             --input="$variant.input_vcf"
             --format=snpeff
         #else
             --input="$variant.input_tsv"
            --pos_column=$variant.pos_column
            --ref_column=$variant.ref_column
            --alt_column=$variant.alt_column
            --transcript_column=$variant.transcript_column
            --dp_column=$variant.dp_column
            --dpr_column=$variant.dpr_column
         #end if
         #if str($filter.min_depth) != '':
             --min_depth=$filter.min_depth
         #end if
         #if str($filter.min_freq) != '':
             --min_freq=$filter.min_freq
         #end if
         #if str($report.readthrough) != '':
             --readthrough=$report.readthrough
         #end if
         #if str($report.leading_aa) != '':
             --leading_aa=$report.leading_aa
         #end if
         #if str($report.trailing_aa) != '':
             --trailing_aa=$report.trailing_aa
         #end if
         --output="$output"
    ]]></command>
    <inputs>
        <conditional name="variant">
            <param name="fmt" type="select" label="Input format for variants">
                <option value="vcf">snpEff vcf</option>
                <option value="tsv">tabular from snpsift extract</option>
            </param>
            <when value="vcf">
                <param name="input_vcf" type="data" format="vcf" label="snpEff VCF file"/>
            </when>
            <when value="tsv">
                <param name="input_tsv" type="data" format="tabular" label="tabular file"/>
                <param name="pos_column" type="data_column" data_ref="input_tsv" label="POS column"/>
                <param name="ref_column" type="data_column" data_ref="input_tsv" label="REF column"/>
                <param name="alt_column" type="data_column" data_ref="input_tsv" label="ALT column"/>
                <param name="transcript_column" type="data_column" data_ref="input_tsv" label="Transcript ID column"/>
                <param name="dp_column" type="data_column" data_ref="input_tsv" label="Read Depth (DP) column"/>
                <param name="dpr_column" type="data_column" data_ref="input_tsv" label="Allele Count (DPR ro AN) column"/>
            </when>
        </conditional>
        <conditional name="ref">
            <param name="ref_source" type="select" label="Source for Genomic Data">
                <option value="cached">Locally cached</option>
                <option value="history">History</option>
            </param>
            <when value="cached">
                <param name="ref_loc" type="select" label="Select reference 2bit file">
                    <options from_data_table="twobit" />
                </param>
            </when>
            <when value="history">
                <param name="ref_file" type="data" format="twobit" label="reference 2bit file" />
            </when>
        </conditional>
        <param name="gtf_file" type="data" format="gtf" label="Ensembl GTF file"/>
        <section name="filter" expanded="false" title="Filter Options">
            <param name="min_depth" type="integer" value="" optional="true" min="0" label="Minimum Read Depth to report" 
                   help="If a value is entered, ignore variants with DP INFO field less than this value"/>
            <param name="min_freq" type="float" value="" optional="true" min="0.0" max="1.0" label="Minimum Alt frequency to report"
                   help="If a value is entered, ignore variant alleles where its DPR count divided the sum of DPR is less than this value"/>
        </section>
        <section name="report" expanded="false" title="Report Options">
            <param name="readthrough" type="integer" value="0" optional="true" min="0" max="4" label="Number of readthrough stop codons to display"/>
            <param name="leading_aa" type="integer" value="10" optional="true" min="0" label="Number of Amino Acids prior to variant to display"
                   help="Ignored for frame shifts"/>
            <param name="trailing_aa" type="integer" value="10" optional="true" min="0" label="Number of Amino Acids following the variant to display"
                   help="Ignored for frame shifts"/>
        </section>
        
    </inputs>
    <outputs>
        <data name="output" format="tabular" >
            <actions>
                <action name="column_names" type="metadata" 
                 default="Gene,Ref_location,Ref_seq,Var_seq,Frequency,DP,Ensemble_Gene_transcript,AA_pos,AA_var,Protein_len,Stop_Codon,Variant_Peptide,Transcipt_type"/>
            </actions>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="fmt" value="vcf"/>
            <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/>
            <param name="ref_source" value="history"/>
            <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
            <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
            <output name="output">
                <assert_contents>
                    <has_text text="MGGQ_A_SASNSFSRLH" />
                    <not_has_text text="*REDHAAGPEA" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="fmt" value="vcf"/>
            <param name="input_vcf" value="GRCh38_X400k_EFF.vcf" ftype="vcf"/>
            <param name="ref_source" value="history"/>
            <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
            <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
            <output name="output">
                <assert_contents>
                    <has_text text="MGGQ_A_SASNSFSRLH" />
                    <not_has_text text="*REDHAAGPEA" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="fmt" value="vcf"/>
            <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/>
            <param name="ref_source" value="history"/>
            <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
            <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
            <param name="readthrough" value="1"/>
            <output name="output">
                <assert_contents>
                    <has_text text="MGGQ_A_SASNSFSRLH" />
                    <has_text text="*REDHAAGPEA" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="fmt" value="vcf"/>
            <param name="input_vcf" value="GRCh38_X400k_ANN.vcf" ftype="vcf"/>
            <param name="ref_source" value="history"/>
            <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
            <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
            <param name="min_depth" value="100"/>
            <param name="min_freq" value=".80"/>
            <output name="output">
                <assert_contents>
                    <has_text text="EQLDAGVRYL_E_LRIAHMLEGS" />
                    <not_has_text text="EYDILVAEET_V_GEPWEDGFEA" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="fmt" value="tsv"/>
            <param name="input_tsv" value="GRCh38_X400k.tsv" ftype="tabular"/>
            <param name="ref_source" value="history"/>
            <param name="ref_file" value="GRCh38_X.2bit" ftype="twobit"/>
            <param name="gtf_file" value="GRCh38_X.83.gtf" ftype="gtf"/>
            <param name="pos_column" value="2"/>
            <param name="ref_column" value="3"/>
            <param name="alt_column" value="4"/>
            <param name="transcript_column" value="7"/>
            <param name="dp_column" value="8"/>
            <param name="dpr_column" value="9"/>
            <output name="output">
                <assert_contents>
                    <has_text text="MGGQ_A_SASNSFSRLH" />
                    <not_has_text text="*REDHAAGPEA" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
Uses an Essembl GTF and a genome 2bit reference to report variant peptides from snpEff reported missense and frameshift variants.
Allows readthrough of stop codons, and reports the stop codons.  

Input can be a snpEff vcf file using either ANN or EFF annotations.
Alternatively, the input can be a tabular file that has columns:

  - pos
  - ref
  - alt
  - Ensembl Transcript ID
  - Read Depth (DP)
  - AlleleDepth (DPR)

    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btt385</citation>
    </citations>
</tool>