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<tool id="edu.tamu.cpt2.spanin.generate-putative-osp" name="OSP candidates" version="1.0">
    <description>constructs a putative list of potential o-spanin from an input genomic FASTA</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="3.9">python</requirement>
        <requirement type="package" version="1.84">biopython</requirement>
        <requirement type="package" version="2024.9.11">regex</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
'$__tool_directory__/generate-putative-osp.py'
'$fasta_file'
--strand '$strand'
--switch '$switch'
--osp_on '$osp_on'
--osp_op '$osp_op'
--osp_ob '$osp_ob'
--osp_og '$osp_og'
--osp_min_len '$osp_min_len'
--putative_osp '$putative_osp'
--summary_osp_txt '$summary_osp'
--putative_osp_gff '$putative_osp_gff'
--min_lipo_after '$lipo_min'
--max_lipo_after '$lipo_max'
--osp_max '$osp_max'
]]></command>
    <inputs>
        <param type="select" label="Strand Choice" name="strand">
            <option value="both">both</option>
            <option value="forward">+</option>
            <option value="reverse">-</option>
        </param>
        <param label="Single Genome FASTA" name="fasta_file" type="data" format="fasta"/>
        <param label="o-spanin minimal length" name="osp_min_len" type="integer" value="45"/>
        <param label="o-spanin maximum length" name="osp_max" type="integer" value="200"/>
        <param label="Range Selection; default is all; for a specific range to check for a spanin input integers separated by a colon (eg. 1234:4321)" type="text" name="switch" value="all"/>
        <param label="Lipobox minimal distance from start codon" name="osp_min_dist" type="integer" value="10"/>
        <param label="Lipobox maximum distance from start codon" name="osp_max_dist" type="integer" value="60" help="Searches for a Lipobox between Lipoboxmin and Lipoboxmax ie [Lipoboxmin,Lipoboxmax]"/>
        <param label="Minimum amount of residues after lipobox is found" name="lipo_min" type="integer" value="25"/>
        <param label="Maximum amount of residues after lipobox is found" name="lipo_max" type="integer" value="170"/>
    </inputs>
    <outputs>
        <data format="fasta" name="osp_on" label="NucSequences.fa" hidden="true"/>
        <data format="fasta" name="osp_op" label="ProtSequences.fa" hidden="true"/>
        <data format="bed" name="osp_ob" label="BED_Output.bed" hidden="true"/>
        <data format="gff3" name="osp_og" label="GFF_Output.gff" hidden="true"/>
        <data format="fasta" name="putative_osp" label="putative_osp.fa"/>
        <data format="txt" name="summary_osp" label="summary_osp.txt"/>
        <data format="gff3" name="putative_osp_gff" label="putative_osp.gff3"/>
    </outputs>
    <help><![CDATA[

**What it does**
Searches a genome for candidate o-spanins (OSPs), a phage protein involved in outer membrane disruption during Gram-negative bacterial host cell lysis.


**METHODOLOGY**

Locates ALL potential start sequences, based on TTG / ATG / GTG (M / L / V). This list is pared down to those within the user-set min/max lengths. That filtered list generates a set of files with the ORFs in FASTA (nt and aa), BED, and GFF3 file formats.

For each sequence in the protein FASTA, the tool then checks within the user-specified range (min/max distance from start codon) for a regular expression (RegEx) to identify a potential lipobox. The following residues are allowed for the potential lipobox: 

    * [ILMFTV][^REKD][GAS]C
    * AW[AGS]C

Finally, the protein list is filtered for size with user-set periplasmic length parameters, calculated as the number of residues after the putative lipobox.

**INPUT** --> Genomic FASTA
*NOTE: This tool only takes a SINGLE genomic fasta. It does not work with multiFASTAs.*

**OUTPUT** --> putative_osp.fa (FASTA) file, putative_osp.gff3, and basic summary statistics file as sumamry_osp.txt
Protein sequences which passed the above filters are returned as the candidate OSPs.
]]></help>
    <expand macro="citations-crr"/>
</tool>