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<tool id="edu.tamu.cpt.sar.sar_finder" name="SAR Finder" version="1.0">
    <description>SAR Domain Finder</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
    </expand>
    <command detect_errors="aggressive"><![CDATA[
python '$__tool_directory__/SAR_finder.py'
'$fa'
--sar_min '$sar_min'
--sar_max '$sar_max'
--out_fa '$out_fa'
--out_gff3 '$out_gff3'
--out_stat '$out_stat'
    ]]></command>
    <inputs>
        <param label="Multi FASTA File" name="fa" type="data" format="fasta"/>
        <param label="SAR domain minimal size" name="sar_min" type="integer" value="15"/>
        <param label="SAR domain maximum size" name="sar_max" type="integer" value="20"/>
    </inputs>
    <outputs>
        <data format="tabular" name="out_stat" label="candidate_SAR_stats.tsv"/>
        <data format="fasta" name="out_fa" label="candidate_SAR.fa"/>
        <data format="gff3" name="out_gff3" label="candidate_SAR.gff3"/>
    </outputs>
    <tests>
        <test>
            <param name="fa" value="simple-proteins.fa"/>
            <param name="sar_min" value="15"/>
            <param name="sar_max" value="20"/>
            <output name="out_stat" file="candidate_SAR_stats.tsv"/>
            <output name="out_fa" file="candidate_SAR.fa"/>
            <output name="out_gff3" file="candidate_SAR.gff3"/>
        </test>
    </tests>
    <help><![CDATA[

**What it does**
A tool that analyzes the sequence within the first 50 residues of a protein for a weakly hydrophobic domain called Signal-Anchor-Release (aka SAR). 
The tool finds proteins that contain a stretch (default 15-20 residues) of hydrophobic residues (Ile, Leu, Val, Phe, Tyr, Trp, Met, Gly, Ala, Ser) and 
calculates the % Gly/Ala/Ser/Thr residues in the hydrophobic stretch. The net charge on the N-terminus is also displayed to aid in determining the 
SAR orientation in the membrane.[2]

Definition: A Signal-Anchor-Release (SAR) domain is an N-terminal, weakly hydrophobic transmembrane region rich in Gly/Ala and/or Ser (and sometimes Thr) residues. 
The SAR domain is sometimes found in phage lysis proteins, including endolysins and holins. The SAR domain can be released from the membrane in a proton 
motive force-dependent manner. Known SAR domains in phage endolysins often have >50-60% Gly/Ala/Ser/Thr content. SAR endolysins are expected to have a net positive
charge on the N-terminus by the positive-inside rule.

**INPUT** --> Protein Multi FASTA

**OUTPUT** --> 

* Multi FASTA with candidate proteins that pass the SAR domain criteria

* Tabular summary file that lists every subdomain fitting the criteria for each potential SAR domain-containing protein with the following: protein name/sequence/length, SAR length/start/sequence/end, individual and total GAST% content in SAR, and N-terminal sequence/net charge

* Multi GFF3 for unique candidate SAR domain-containing proteins

    ]]></help>
    <citations>
        <citation type="doi">10.1371/journal.pcbi.1008214</citation>
        <citation type="doi">https://dx.doi.org/10.1016/bs.aivir.2018.09.003</citation>
        <citation type="bibtex">
            @unpublished{galaxyTools,
            author = {C. Ross},
            title = {CPT Galaxy Tools},
            year = {2020-},
            note = {https://github.com/tamu-cpt/galaxy-tools/}
            }
        </citation>
    </citations>
</tool>