comparison blast_annotations_processor.xml @ 1:2acf82433aa4 draft default tip

planemo upload for repository https://github.com/Onnodg/Naturalis_NLOOR/tree/main/NLOOR_scripts/process_annotations_tool commit d771f9fbfd42bcdeda1623d954550882a0863847-dirty

0:a3989edf0a4a

<tool id="blast_annotation_processor" name="BLAST Annotation Processor" version="1.0.0">
    <description>Process BLAST annotation results with taxonomic analysis</description>

    <requirements>
        <requirement type="package" version="3.12.3">python</requirement>
        <requirement type="package" version="3.10.6">matplotlib</requirement>

        <param name="outputs" type="select" multiple="true" display="checkboxes"
               label="Select outputs to generate" help="Choose which analysis outputs to create">
            <option value="eval_plot">E-value distribution plot</option>
            <option value="taxa_output">Taxonomic report (Kraken2-like format)</option>
            <option value="circle_data">Circular taxonomic datafile</option>
            <option value="header_anno">Header annotations table</option>
            <option value="anno_stats">Annotation statistics</option>
        </param>

        <!-- Processing Parameters -->
        <section name="advanced" title="Advanced Parameters" expanded="false">

- **Taxonomic report**: Kraken2-like format report showing taxonomic composition with read counts and percentages. Includes information about uncertain taxonomic assignments.

- **Circular taxonomic data**: Json data to generate a circular sunburst-style diagram showing taxonomic composition across all taxonomic levels (Kingdom -> Species).

- **Header annotations table**: Excel workbook listing each sequence header with its taxonomic assignment and E-value.

- **Annotation statistics**: Summary statistics about annotation success rates and sequence counts.

**Parameters:**

- **Uncertain threshold**: When multiple conflicting taxonomic assignments exist for a sequence, this threshold determines whether to use the most common assignment (if it exceeds the threshold) or mark it as "Uncertain taxa".

- **E-value threshold**: Sequences with E-values higher than this threshold are filtered out from the analysis.

- **Use read counts**: Determines whether circular data reflects the abundance of reads (checked) or just count unique taxonomic assignments (unchecked).
#Query ID	#Subject	#Subject accession	#Subject Taxonomy ID	#Identity percentage
	#Coverage	#evalue	#bitscore	#Source	#Taxonomy
**Expected Input Format:**

The annotated BLAST file should be in tabular format with at least 7 columns:
1. Query ID
2. Subject ID
3. Subject accession
4. Subject Taxonomy ID
5. Identity percentage
6. Coverage
7. Evalue
8. Bitscore
9. Source
10. Taxonomy

**Note:** This tool processes files that have been deduplicated and contain read count information in the sequence headers in the format: `sequence_name(count_number)`.

**Credits**
Authors = Onno de Gorter, 2025.
Based on a script by Nick Kortleven, translated, modified and wrapped by Onno de Gorter,
Developed for the New light on old remedies project, a PhD research by Anja Fischer
    ]]></help>
</tool>

1:2acf82433aa4

<tool id="blast_annotation_processor" name="BLAST Annotation Processor" version="1.0.1">
    <description>Process BLAST annotation results with taxonomic analysis</description>

    <requirements>
        <requirement type="package" version="3.12.3">python</requirement>
        <requirement type="package" version="3.10.6">matplotlib</requirement>

        <param name="outputs" type="select" multiple="true" display="checkboxes"
               label="Select outputs to generate" help="Choose which analysis outputs to create">
            <option value="eval_plot">E-value distribution plot</option>
            <option value="taxa_output">Taxonomic report (Kraken2-like format)</option>
            <option value="circle_data">Circular taxonomic datafile</option>
            <option value="header_anno">Annotations per header (in Excel)</option>
            <option value="anno_stats">Annotation statistics</option>
        </param>

        <!-- Processing Parameters -->
        <section name="advanced" title="Advanced Parameters" expanded="false">

- **Taxonomic report**: Kraken2-like format report showing taxonomic composition with read counts and percentages. Includes information about uncertain taxonomic assignments.

- **Circular taxonomic data**: Json data to generate a circular sunburst-style diagram showing taxonomic composition across all taxonomic levels (Kingdom -> Species).

- **Annotations per header**: Excel workbook listing each sequence header with its taxonomic assignment and E-value.

- **Annotation statistics**: Summary statistics about annotation success rates and sequence counts.

**Parameters:**

- **Uncertain threshold**: Treshold for lca. When multiple conflicting taxonomic assignments exist for a sequence, this threshold determines whether to use the most common assignment (if it exceeds the threshold) or mark it as "Uncertain taxa".

- **E-value threshold**: Sequences with E-values higher than this threshold are filtered out from the analysis.

- **Use read counts**: Determines whether circular data reflects the abundance of reads (checked) or just count unique taxonomic assignments (unchecked).

**Expected Input Format:**

The annotated BLAST file should be in tabular format with at least 7 columns:

- 1. Query ID

- 2. Subject ID

- 3. Subject accession

- 4. Subject Taxonomy ID

- 5. Identity percentage

- 6. Coverage

- 7. Evalue

- 8. Bitscore

- 9. Source

- 10. Taxonomy

**Note:** This tool processes files that have been deduplicated and contain read count information in the sequence headers in the format: `sequence_name(count_number)`.

-------------

.. class:: infomark

**Credits**

Based on a script by Nick Kortleven, translated, modified and wrapped by Onno de Gorter,
Developed for the New light on old remedies project, a PhD research by Anja Fischer.

Link to the project website:

* https://ahm.uva.nl/funded-research-projects/new-lights-on-old-remedies/new-lights-on-old-remedies.html

    ]]></help>
    <creator>
        <organization name="Naturalis Biodiversity Center" url="https://www.naturalis.nl/en/science" />
        <person givenName="Onno" familyName="de Gorter" url="https://github.com/Onnodg"/>
        <person givenName="Nick" familyName="Kortleven" url="https://github.com/tombkingsts" />
    </creator>
</tool>