<tool id="bed_to_protein_map" name="bed to protein map" version="0.2.0">
    <description>genomic location of proteins for MVP</description>
    <requirements>
        <requirement type="package" version="3.7">python</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        python '$__tool_directory__/bed_to_protein_map.py' '$input' '$output'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="bed" label="A BED file with 12 columns, thickStart and thickEnd define protein coding region"/>
    </inputs>
    <outputs>
        <data name="output" format="tabular">
            <actions>
                <action name="column_names" type="metadata" default="name,chrom,start,end,strand,cds_start,cds_end"/>
            </actions>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" ftype="bed" value="input.bed"/>
            <output name="output" file="output.tabular"/>
        </test>
    </tests>
    <help><![CDATA[
Convert a BED format file of the proteins from a proteomics search database into a tabular format for the Multiomics Visualization Platform (MVP).

Example input BED dataset::

	X	276352	291629	ENST00000430923	20	+	284187	291629	80,80,80	5	42,148,137,129,131	0,7814,12380,14295,15146
	X	304749	318819	ENST00000326153	20	-	305073	318787	80,80,80	10	448,153,149,209,159,68,131,71,138,381	0,2610,2982,6669,8016,9400,10140,10479,12164,13689


Output::

    name               chrom   start     end       strand  cds_start  cds_end
    ENST00000430923    X       284187    284314    +          0        127
    ENST00000430923    X       288732    288869    +        127        264
    ENST00000430923    X       290647    290776    +        264        393
    ENST00000430923    X       291498    291629    +        393        524
    ENST00000326153    X       318438    318787    -          0        349
    ENST00000326153    X       316913    317051    -        349        487
    ENST00000326153    X       315228    315299    -        487        558
    ENST00000326153    X       314889    315020    -        558        689
    ENST00000326153    X       314149    314217    -        689        757
    ENST00000326153    X       312765    312924    -        757        916
    ENST00000326153    X       311418    311627    -        916       1125
    ENST00000326153    X       307731    307880    -       1125       1274
    ENST00000326153    X       307359    307512    -       1274       1427
    ENST00000326153    X       305073    305197    -       1427       1551


The tabular output can be converted to a sqlite database using the Query_Tabular_ tool.

The sqlite table should be named:  feature_cds_map
The names for the columns should be: name,chrom,start,end,strand,cds_start,cds_end

This SQL query will return the genomic location for a peptide sequence in a protein (multiply the animo acid position by 3 for the cds location)::

    SELECT distinct chrom, CASE WHEN strand = '+' THEN start + cds_offset - cds_start ELSE end - cds_offset - cds_start END as "pos"
    FROM feature_cds_map
    WHERE name = acc_name AND cds_offset >= cds_start AND cds_offset < cds_end


.. _Query_Tabular: https://toolshed.g2.bx.psu.edu/view/iuc/query_tabular/1ea4e668bf73

    ]]></help>
</tool>