Mercurial > repos > cpt > cpt_annotation_table
diff phage_annotation_table.xml @ 1:32e011fa615c draft
planemo upload commit edc74553919d09dcbe27fcadf144612c1ad3a2a2
| author | cpt |
|---|---|
| date | Wed, 26 Apr 2023 03:42:32 +0000 |
| parents | |
| children | 83af8dfd079d |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phage_annotation_table.xml Wed Apr 26 03:42:32 2023 +0000 @@ -0,0 +1,104 @@ +<tool id="edu.tamu.cpt2.phage.annotation_table" name="Annotation Table" version="20.0.0.1"> + <description>from gff3 formatted datasets</description> + <macros> + <import>macros.xml</import> + <import>cpt-macros.xml</import> + </macros> + <expand macro="requirements"> + <requirement type="package" version="2.10.1">jinja2</requirement> + </expand> + <command detect_errors="aggressive"><![CDATA[ +@GENOME_SELECTOR_PRE@ + +python '$__tool_directory__/phage_annotation_table.py' +'$gff3_data' +@GENOME_SELECTOR@ +--types "$extraTypes" +--reportTemplateName "$report_format" +--annotationTableCols "$cols,$gaf_cols" +#if $gaf_data: +--gafData "$gaf_data" +#end if +'$checkSubfeats' +> '$output']]></command> + <inputs> + <expand macro="gff3_input"/> + <expand macro="genome_selector"/> + <param label="Extra sub-feature types to include (Comma-separated, Will always include gene)" optional="True" name="extraTypes" type="text" value=""/> + <param label="Columns" type="select" name="cols" multiple="True"> + <option value="rid" selected="true">Record ID</option> + <option value="id" selected="true">ID</option> + <option value="type" selected="true">Type</option> + <option value="name" selected="true">Name</option> + <option value="location" selected="true">Location</option> + <option value="start" selected="true">Feature Start</option> + <option value="end" selected="true">Feature End</option> + <option value="strand" selected="true">Strand</option> + <option value="length" selected="true">Length</option> + <option value="sd_seq" selected="true">SD sequence</option> + <option value="sd_spacing" selected="true">SD spacing</option> + <option value="start_codon" selected="true">Start codon</option> + <option value="stop_codon" selected="true">Stop codon</option> + <option value="ig_dist" selected="true">Distance to next upstream feature</option> + <option value="upstream_feature__name" selected="true">Name of upstream feature</option> + <option value="owner" selected="true">Owner</option> + <option value="date_created" selected="true">Date created</option> + <option value="date_last_modified" selected="true">Date last modified</option> + <option value="notes" selected="true">Notes</option> + <option value="description" selected="true">Description</option> + <option value="product" selected="true">Product</option> + <option value="dbxrefs" selected="true">DBxrefs</option> + <option value="qualifiers" selected="true">Qualifiers</option> + </param> + <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."/> + <param label="GAF Columns" type="select" name="gaf_cols" multiple="True"> + <!-- GAF Specific Fields --> + <option value="gaf_annotation_extension" selected="false">GAF Annotation Extension</option> + <option value="gaf_aspect" selected="false">GAF Aspect</option> + <option value="gaf_assigned_by" selected="false">GAF Assigned By</option> + <option value="gaf_date" selected="false">GAF Date</option> + <option value="gaf_db" selected="false">GAF DB</option> + <option value="gaf_db_reference" selected="false">GAF DB Reference</option> + <option value="gaf_evidence_code" selected="false">GAF Evidence Code</option> + <option value="gaf_gene" selected="false">GAF Gene</option> + <option value="gaf_go_id" selected="false">GAF GO ID</option> + <option value="gaf_go_term" selected="false">GAF GO Term</option> + <option value="gaf_id" selected="false">GAF ID</option> + <option value="gaf_notes" selected="false">GAF Notes</option> + <option value="gaf_owner" selected="false">GAF Owner</option> + <option value="gaf_with_or_from" selected="false">GAF with_or_from</option> + </param> + <param name="checkSubfeats" label="Search sub-features for fields if gene does not define them" type="boolean" truevalue="--searchSubs" falsevalue=""/> + <param label="Report Format" type="select" name="report_format"> + <option value="phageqc_report_annotation_table.html" selected="true">HTML Table</option> + <option value="phageqc_report_annotation_table.tsv">Tabular (Excel Compatible) Table</option> + </param> + </inputs> + <outputs> + <data format="html" name="output"> + <change_format> + <when format="tabular" input="report_format" value="phageqc_report_annotation_table.tsv"/> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="reference_genome_source" value="history"/> + <param name="genome_fasta" value="NC_001416_Table_In.fasta"/> + <param name="gff3_data" value="NC_001416_Table_In.gff3"/> + <param name="report_format" value="phageqc_report_annotation_table.html"/> + <output name="output" file="PhageTable_Out.html"/> + </test> + <test> + <param name="reference_genome_source" value="history"/> + <param name="genome_fasta" value="NC_001416_Table_In.fasta"/> + <param name="gff3_data" value="NC_001416_Table_In.gff3"/> + <param name="report_format" value="phageqc_report_annotation_table.tsv"/> + <output name="output" file="PhageTable_Out.tabular"/> + </test> + </tests> + <help><![CDATA[ +Generate an "annotation table" of a genome, with user-configurable data columns +]]></help> + <expand macro="citations"/> +</tool>