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comparison phage_annotation_table.xml @ 1:32e011fa615c draft

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planemo upload commit edc74553919d09dcbe27fcadf144612c1ad3a2a2
author cpt
date Wed, 26 Apr 2023 03:42:32 +0000
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0:6a4d1bd8ac1d 1:32e011fa615c
1 <tool id="edu.tamu.cpt2.phage.annotation_table" name="Annotation Table" version="20.0.0.1">
2 <description>from gff3 formatted datasets</description>
3 <macros>
4 <import>macros.xml</import>
5 <import>cpt-macros.xml</import>
6 </macros>
7 <expand macro="requirements">
8 <requirement type="package" version="2.10.1">jinja2</requirement>
9 </expand>
10 <command detect_errors="aggressive"><![CDATA[
11 @GENOME_SELECTOR_PRE@
12
13 python '$__tool_directory__/phage_annotation_table.py'
14 '$gff3_data'
15 @GENOME_SELECTOR@
16 --types "$extraTypes"
17 --reportTemplateName "$report_format"
18 --annotationTableCols "$cols,$gaf_cols"
19 #if $gaf_data:
20 --gafData "$gaf_data"
21 #end if
22 '$checkSubfeats'
23 > '$output']]></command>
24 <inputs>
25 <expand macro="gff3_input"/>
26 <expand macro="genome_selector"/>
27 <param label="Extra sub-feature types to include (Comma-separated, Will always include gene)" optional="True" name="extraTypes" type="text" value=""/>
28 <param label="Columns" type="select" name="cols" multiple="True">
29 <option value="rid" selected="true">Record ID</option>
30 <option value="id" selected="true">ID</option>
31 <option value="type" selected="true">Type</option>
32 <option value="name" selected="true">Name</option>
33 <option value="location" selected="true">Location</option>
34 <option value="start" selected="true">Feature Start</option>
35 <option value="end" selected="true">Feature End</option>
36 <option value="strand" selected="true">Strand</option>
37 <option value="length" selected="true">Length</option>
38 <option value="sd_seq" selected="true">SD sequence</option>
39 <option value="sd_spacing" selected="true">SD spacing</option>
40 <option value="start_codon" selected="true">Start codon</option>
41 <option value="stop_codon" selected="true">Stop codon</option>
42 <option value="ig_dist" selected="true">Distance to next upstream feature</option>
43 <option value="upstream_feature__name" selected="true">Name of upstream feature</option>
44 <option value="owner" selected="true">Owner</option>
45 <option value="date_created" selected="true">Date created</option>
46 <option value="date_last_modified" selected="true">Date last modified</option>
47 <option value="notes" selected="true">Notes</option>
48 <option value="description" selected="true">Description</option>
49 <option value="product" selected="true">Product</option>
50 <option value="dbxrefs" selected="true">DBxrefs</option>
51 <option value="qualifiers" selected="true">Qualifiers</option>
52 </param>
53 <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."/>
54 <param label="GAF Columns" type="select" name="gaf_cols" multiple="True">
55 <!-- GAF Specific Fields -->
56 <option value="gaf_annotation_extension" selected="false">GAF Annotation Extension</option>
57 <option value="gaf_aspect" selected="false">GAF Aspect</option>
58 <option value="gaf_assigned_by" selected="false">GAF Assigned By</option>
59 <option value="gaf_date" selected="false">GAF Date</option>
60 <option value="gaf_db" selected="false">GAF DB</option>
61 <option value="gaf_db_reference" selected="false">GAF DB Reference</option>
62 <option value="gaf_evidence_code" selected="false">GAF Evidence Code</option>
63 <option value="gaf_gene" selected="false">GAF Gene</option>
64 <option value="gaf_go_id" selected="false">GAF GO ID</option>
65 <option value="gaf_go_term" selected="false">GAF GO Term</option>
66 <option value="gaf_id" selected="false">GAF ID</option>
67 <option value="gaf_notes" selected="false">GAF Notes</option>
68 <option value="gaf_owner" selected="false">GAF Owner</option>
69 <option value="gaf_with_or_from" selected="false">GAF with_or_from</option>
70 </param>
71 <param name="checkSubfeats" label="Search sub-features for fields if gene does not define them" type="boolean" truevalue="--searchSubs" falsevalue=""/>
72 <param label="Report Format" type="select" name="report_format">
73 <option value="phageqc_report_annotation_table.html" selected="true">HTML Table</option>
74 <option value="phageqc_report_annotation_table.tsv">Tabular (Excel Compatible) Table</option>
75 </param>
76 </inputs>
77 <outputs>
78 <data format="html" name="output">
79 <change_format>
80 <when format="tabular" input="report_format" value="phageqc_report_annotation_table.tsv"/>
81 </change_format>
82 </data>
83 </outputs>
84 <tests>
85 <test>
86 <param name="reference_genome_source" value="history"/>
87 <param name="genome_fasta" value="NC_001416_Table_In.fasta"/>
88 <param name="gff3_data" value="NC_001416_Table_In.gff3"/>
89 <param name="report_format" value="phageqc_report_annotation_table.html"/>
90 <output name="output" file="PhageTable_Out.html"/>
91 </test>
92 <test>
93 <param name="reference_genome_source" value="history"/>
94 <param name="genome_fasta" value="NC_001416_Table_In.fasta"/>
95 <param name="gff3_data" value="NC_001416_Table_In.gff3"/>
96 <param name="report_format" value="phageqc_report_annotation_table.tsv"/>
97 <output name="output" file="PhageTable_Out.tabular"/>
98 </test>
99 </tests>
100 <help><![CDATA[
101 Generate an "annotation table" of a genome, with user-configurable data columns
102 ]]></help>
103 <expand macro="citations"/>
104 </tool>