annotate phage_annotation_table.xml @ 5:c618332f2386 draft

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date Fri, 24 May 2024 04:42:01 +0000
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1 <tool id="edu.tamu.cpt2.phage.annotation_table" name="Annotation Table" version="20.0.0.1">
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2 <description>from gff3 formatted datasets</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="2.10.1">jinja2</requirement>
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8 </expand>
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9 <command detect_errors="aggressive"><![CDATA[
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10 @GENOME_SELECTOR_PRE@
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11
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12 python '$__tool_directory__/phage_annotation_table.py'
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13 '$gff3_data'
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14 @GENOME_SELECTOR@
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15 --reportTemplateName "$report_format"
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16 --annotationTableCols "$cols,$gaf_cols"
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17 #if $extraTypes:
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18 --types "$extraTypes"
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19 #end if
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20 #if $gaf_data:
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21 --gafData "$gaf_data"
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22 #end if
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23 '$checkSubfeats'
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24 > '$output']]></command>
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25 <inputs>
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26 <expand macro="gff3_input"/>
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27 <expand macro="genome_selector"/>
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28 <param label="Extra sub-feature types to include (Comma-separated, Will always include gene)" optional="True" name="extraTypes" type="text" value=""/>
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29 <param label="Columns" type="select" name="cols" multiple="True">
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30 <option value="rid" selected="true">Record ID</option>
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31 <option value="id" selected="true">ID</option>
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32 <option value="type" selected="true">Type</option>
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33 <option value="name" selected="true">Name</option>
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34 <option value="location" selected="true">Location</option>
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35 <option value="start" selected="true">Feature Start</option>
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36 <option value="end" selected="true">Feature End</option>
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37 <option value="strand" selected="true">Strand</option>
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38 <option value="length" selected="true">Length</option>
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39 <option value="sd_seq" selected="true">SD sequence</option>
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40 <option value="sd_spacing" selected="true">SD spacing</option>
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41 <option value="start_codon" selected="true">Start codon</option>
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42 <option value="stop_codon" selected="true">Stop codon</option>
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43 <option value="ig_dist" selected="true">Distance to next upstream feature</option>
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44 <option value="upstream_feature__name" selected="true">Name of upstream feature</option>
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45 <option value="owner" selected="true">Owner</option>
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46 <option value="date_created" selected="true">Date created</option>
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47 <option value="date_last_modified" selected="true">Date last modified</option>
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48 <option value="notes" selected="true">Notes</option>
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49 <option value="description" selected="true">Description</option>
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50 <option value="product" selected="true">Product</option>
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51 <option value="dbxrefs" selected="true">DBxrefs</option>
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52 <option value="qualifiers" selected="true">Qualifiers</option>
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53 </param>
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54 <param label="GAF Data" name="gaf_data" type="data" format="tabular" optional="True" help="Optional GAF Data Table. This usually comes from the CPT CACAO GAF Data Export tool. The [GAF] Columns below are ONLY available when this data is populated."/>
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55 <param label="GAF Columns" type="select" name="gaf_cols" multiple="True">
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56 <!-- GAF Specific Fields -->
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57 <option value="gaf_annotation_extension" selected="false">GAF Annotation Extension</option>
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58 <option value="gaf_aspect" selected="false">GAF Aspect</option>
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59 <option value="gaf_assigned_by" selected="false">GAF Assigned By</option>
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60 <option value="gaf_date" selected="false">GAF Date</option>
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61 <option value="gaf_db" selected="false">GAF DB</option>
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62 <option value="gaf_db_reference" selected="false">GAF DB Reference</option>
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63 <option value="gaf_evidence_code" selected="false">GAF Evidence Code</option>
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64 <option value="gaf_gene" selected="false">GAF Gene</option>
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65 <option value="gaf_go_id" selected="false">GAF GO ID</option>
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66 <option value="gaf_go_term" selected="false">GAF GO Term</option>
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67 <option value="gaf_id" selected="false">GAF ID</option>
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68 <option value="gaf_notes" selected="false">GAF Notes</option>
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69 <option value="gaf_owner" selected="false">GAF Owner</option>
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70 <option value="gaf_with_or_from" selected="false">GAF with_or_from</option>
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71 </param>
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72 <param name="checkSubfeats" label="Search sub-features for fields if gene does not define them" type="boolean" truevalue="--searchSubs" falsevalue=""/>
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73 <param label="Report Format" type="select" name="report_format">
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74 <option value="phageqc_report_annotation_table.html" selected="true">HTML Table</option>
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75 <option value="phageqc_report_annotation_table.tsv">Tabular (Excel Compatible) Table</option>
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76 </param>
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77 </inputs>
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78 <outputs>
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79 <data format="html" name="output">
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80 <change_format>
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81 <when format="tabular" input="report_format" value="phageqc_report_annotation_table.tsv"/>
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82 </change_format>
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83 </data>
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84 </outputs>
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85 <tests>
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86 <test>
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87 <param name="reference_genome_source" value="history"/>
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88 <param name="genome_fasta" value="NC_001416_Table_In.fasta"/>
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89 <param name="gff3_data" value="NC_001416_Table_In.gff3"/>
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90 <param name="report_format" value="phageqc_report_annotation_table.html"/>
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91 <output name="output" file="PhageTable_Out.html"/>
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92 </test>
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93 <test>
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94 <param name="reference_genome_source" value="history"/>
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95 <param name="genome_fasta" value="NC_001416_Table_In.fasta"/>
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96 <param name="gff3_data" value="NC_001416_Table_In.gff3"/>
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97 <param name="report_format" value="phageqc_report_annotation_table.tsv"/>
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98 <output name="output" file="PhageTable_Out.tabular"/>
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99 </test>
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100 </tests>
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101 <help><![CDATA[
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102 Generate an "annotation table" of a genome, with user-configurable data columns
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103 ]]></help>
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104 <expand macro="citations"/>
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105 </tool>