Mercurial > repos > cpt > cpt_phageqc_annotations
diff cpt_phageqc_annotation/phage_annotation_validator.xml @ 0:c3140b08d703 draft default tip
Uploaded
author | cpt |
---|---|
date | Fri, 17 Jun 2022 13:00:50 +0000 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt_phageqc_annotation/phage_annotation_validator.xml Fri Jun 17 13:00:50 2022 +0000 @@ -0,0 +1,102 @@ +<?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>