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