<?xml version="1.0"?>
<tool id="edu.tamu.cpt2.phage.annotation_validator" name="Phage QC" version="1.9.0" profile="16.04">
    <description>validate phage annotations</description>
    <macros>
      <import>macros.xml</import>
		<import>cpt-macros.xml</import>
    </macros>
    <requirements>
      <requirement type="package" version="3.6">python</requirement>
      <requirement type="package" version="1.77">biopython</requirement>
      <requirement type="package" version="1.1.7">cpt_gffparser</requirement>  
      <requirement type="package" version="0.12.0">python-levenshtein</requirement>
      <requirement type="package" version="2019.06.08">regex</requirement>
      <requirement type="package">metagene_annotator</requirement>
      <requirement type="package" version="2.10.1">jinja2</requirement>
      <requirement type="package" version="1.11">numpy</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
@GENOME_SELECTOR_PRE@

python $__tool_directory__/phage_annotation_validator.py
$gff3_data
@GENOME_SELECTOR@

--gff3 $gff3

--sd_min $sd_min
--sd_max $sd_max

--min_gene_length $min_gene

--excessive_overlap_dist $eod
--excessive_overlap_divergent_dist $eodd

--excessive_gap_dist $egd
--excessive_gap_divergent_dist $egdd

--reportTemplateName $report_format

> $output;

#if ".tex" in str($report_format):
    mv $output tmp.tex;
    docker run --rm -i --user="1002:1002" --net=none -v \$PWD:/data blang/latex pdflatex tmp.tex &&
    docker run --rm -i --user="1002:1002" --net=none -v \$PWD:/data blang/latex pdflatex tmp.tex &&
    mv tmp.pdf $output;
#end if
]]></command>
    <inputs>
        <expand macro="gff3_input" />
        <expand macro="genome_selector" />

        <param label="Minimum distance for SDs (bp)" name="sd_min" type="integer" value="5" />
        <param label="Maximum distance for SDs (bp)" name="sd_max" type="integer" value="15" />

        <param label="Minimum length of naively called ORFs in gaps (in AAs)" name="min_gene" type="integer" value="25" />

        <param label="Excessive overlap distance (non-divergent, bp)" name="eod" type="integer" value="25" />
        <param label="Excessive overlap distance (divergent, bp)" name="eodd" type="integer" value="50" />

        <param label="Excessive gap distance (non-divergent, bp)" name="egd" type="integer" value="50" />
        <param label="Excessive gap distance (divergent, bp)" name="egdd" type="integer" value="200" />

        <param label="Report Format" type="select" name="report_format">
            <option value="phageqc_report_full.html" selected="True">Full Report</option>
            <option value="phageqc_report_464.html">464 Report</option>
            <option value="phageqc_report_genomea.tex">GenomeA PDF Report</option>
            <option value="phageqc_report_genomea.html">GenomeA HTML Report</option>
        </param>
    </inputs>
    <outputs>
      <data format="html" name="output">
          <change_format>
            <when input="report_format" value="phageqc_report_genomea.tex" format="pdf"/>
          </change_format>
      </data>
      <data format="gff3" name="gff3" label="Phage QC annotation track"/>
    </outputs>
    <tests>
      <test>
        <param name="gff3_data" value="AY216660.gff3"/>
        <param name="genome_fasta" value="AY216660.fasta" />
	<output name="gff3" file="PhageQC_Out.gff3"/> 
        <output name="output" file="PhageQC_Out.html"/>
      </test>
    </tests>    
    <help><![CDATA[
**What it does**

Run CPT's Phage Annotation Validator validating the following properties:

-  Missing RBSs
-  Missing Gene Features
-  Excessive Gaps
-  Excessive Overlaps
-  Morons
-  Weird Start Codons
-  Incorrect gene model (when used with our Genbank Gene Model correction tool)

        ]]></help>
		<expand macro="citations" />
</tool>