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comparison cpt_phageqc_annotation/phage_annotation_validator.xml @ 0:c3140b08d703 draft default tip

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author cpt
date Fri, 17 Jun 2022 13:00:50 +0000
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1 <?xml version="1.0"?>
2 <tool id="edu.tamu.cpt2.phage.annotation_validator" name="Phage QC" version="1.9.0" profile="16.04">
3 <description>validate phage annotations</description>
4 <macros>
5 <import>macros.xml</import>
6 <import>cpt-macros.xml</import>
7 </macros>
8 <requirements>
9 <requirement type="package" version="3.6">python</requirement>
10 <requirement type="package" version="1.77">biopython</requirement>
11 <requirement type="package" version="1.1.7">cpt_gffparser</requirement>
12 <requirement type="package" version="0.12.0">python-levenshtein</requirement>
13 <requirement type="package" version="2019.06.08">regex</requirement>
14 <requirement type="package">metagene_annotator</requirement>
15 <requirement type="package" version="2.10.1">jinja2</requirement>
16 <requirement type="package" version="1.11">numpy</requirement>
17 </requirements>
18 <command detect_errors="aggressive"><![CDATA[
19 @GENOME_SELECTOR_PRE@
20
21 python $__tool_directory__/phage_annotation_validator.py
22 $gff3_data
23 @GENOME_SELECTOR@
24
25 --gff3 $gff3
26
27 --sd_min $sd_min
28 --sd_max $sd_max
29
30 --min_gene_length $min_gene
31
32 --excessive_overlap_dist $eod
33 --excessive_overlap_divergent_dist $eodd
34
35 --excessive_gap_dist $egd
36 --excessive_gap_divergent_dist $egdd
37
38 --reportTemplateName $report_format
39
40 > $output;
41
42 #if ".tex" in str($report_format):
43 mv $output tmp.tex;
44 docker run --rm -i --user="1002:1002" --net=none -v \$PWD:/data blang/latex pdflatex tmp.tex &&
45 docker run --rm -i --user="1002:1002" --net=none -v \$PWD:/data blang/latex pdflatex tmp.tex &&
46 mv tmp.pdf $output;
47 #end if
48 ]]></command>
49 <inputs>
50 <expand macro="gff3_input" />
51 <expand macro="genome_selector" />
52
53 <param label="Minimum distance for SDs (bp)" name="sd_min" type="integer" value="5" />
54 <param label="Maximum distance for SDs (bp)" name="sd_max" type="integer" value="15" />
55
56 <param label="Minimum length of naively called ORFs in gaps (in AAs)" name="min_gene" type="integer" value="25" />
57
58 <param label="Excessive overlap distance (non-divergent, bp)" name="eod" type="integer" value="25" />
59 <param label="Excessive overlap distance (divergent, bp)" name="eodd" type="integer" value="50" />
60
61 <param label="Excessive gap distance (non-divergent, bp)" name="egd" type="integer" value="50" />
62 <param label="Excessive gap distance (divergent, bp)" name="egdd" type="integer" value="200" />
63
64 <param label="Report Format" type="select" name="report_format">
65 <option value="phageqc_report_full.html" selected="True">Full Report</option>
66 <option value="phageqc_report_464.html">464 Report</option>
67 <option value="phageqc_report_genomea.tex">GenomeA PDF Report</option>
68 <option value="phageqc_report_genomea.html">GenomeA HTML Report</option>
69 </param>
70 </inputs>
71 <outputs>
72 <data format="html" name="output">
73 <change_format>
74 <when input="report_format" value="phageqc_report_genomea.tex" format="pdf"/>
75 </change_format>
76 </data>
77 <data format="gff3" name="gff3" label="Phage QC annotation track"/>
78 </outputs>
79 <tests>
80 <test>
81 <param name="gff3_data" value="AY216660.gff3"/>
82 <param name="genome_fasta" value="AY216660.fasta" />
83 <output name="gff3" file="PhageQC_Out.gff3"/>
84 <output name="output" file="PhageQC_Out.html"/>
85 </test>
86 </tests>
87 <help><![CDATA[
88 **What it does**
89
90 Run CPT's Phage Annotation Validator validating the following properties:
91
92 - Missing RBSs
93 - Missing Gene Features
94 - Excessive Gaps
95 - Excessive Overlaps
96 - Morons
97 - Weird Start Codons
98 - Incorrect gene model (when used with our Genbank Gene Model correction tool)
99
100 ]]></help>
101 <expand macro="citations" />
102 </tool>