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deploy alphafind on qa1 #313

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220 changes: 220 additions & 0 deletions files/galaxy/tools/alphafind.xml
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<tool id="alphafind_search" name="AlphaFind Protein Search" version="1.0.0">
<description>Search AlphaFind API for structurally similar proteins</description>
<requirements>
<requirement type="package" version="3.6">python</requirement>
<requirement type="package" version="2.31.0">requests</requirement>
</requirements>
<version_command><![CDATA[
python3 '$__tool_directory__/alphafind_search.py' --version 2>/dev/null || echo "1.0.0"
]]></version_command>
<command detect_errors="exit_code"><![CDATA[
python3 '$__tool_directory__/alphafind_search.py'
--query '$query'
#for $idx in $index
--index '$idx'
#end for
#if $filtering.organism
--filter-organism '$filtering.organism'
#end if
#if $filtering.tax_id
--filter-tax-id $filtering.tax_id
#end if
#if $filtering.gene_name
--filter-gene-name '$filtering.gene_name'
#end if
#if $filtering.cath_annotation
--filter-cath-annotation '$filtering.cath_annotation'
#end if
#if $searching.k
--option-k $searching.k
#end if
--timeout ${searching.timeout}
--sort-by ${sorting.sort_by}
--sort-order ${sorting.sort_order}
--quiet
--output '$output'
]]></command>
<inputs>
<!-- Required: Query protein ID -->
<param name="query" type="text" optional="false" label="Protein Query" help="Enter a UniProt protein ID (e.g., P0A6F5, Q8Y547, Q9SBL1)"/>
<!-- Required: Index type selection -->
<param name="index" type="select" label="Search Index" multiple="true" help="Select one or more index types to search. Defaults to all.">
<option value="chains">Chains</option>
<option value="chains_90">Chains 90% identity</option>
<option value="chains_80">Chains 80% identity</option>
<option value="chains_70">Chains 70% identity</option>
<option value="domains">Domains</option>
</param>
<!-- Optional Filters Section -->
<section name="filtering" title="Filtering Options" expanded="false">
<param name="organism" type="text" label="Organism Name" help="Filter by organism name (e.g., 'Mycobacterium tuberculosis')" optional="true"/>
<param name="tax_id" type="integer" label="Taxonomy ID" help="NCBI Taxonomy ID (numeric)" optional="true"/>
<param name="gene_name" type="text" label="Gene Name" help="Filter by gene name" optional="true"/>
<param name="cath_annotation" type="text" label="CATH Annotation" help="Filter by CATH annotation (only applied when using 'domains' index)" optional="true"/>
</section>
<!-- Search Options Section -->
<section name="searching" title="Search Options" expanded="false">
<param name="k" type="integer" label="Number of Similar Proteins" value="10" min="1" max="5000" help="Maximum number of similar proteins to return (k). Note: API can return up to 5000 results."/>
<param name="timeout" type="integer" label="Timeout (seconds)" value="600" min="60" max="3600" help="Maximum time to wait for API to complete the search and computations."/>
</section>
<!-- Sorting Options -->
<section name="sorting" title="Sorting Options" expanded="false">
<param name="sort_by" type="select" label="Sort Results By" help="Choose how to order the results">
<option value="knn">KNN Similarity Score (default)</option>
<option value="tm_score">TM-Score</option>
</param>
<param name="sort_order" type="select" label="Sort Order" help="Choose ascending or descending order">
<option value="desc">Descending (highest first)</option>
<option value="asc">Ascending (lowest first)</option>
</param>
</section>
</inputs>
<outputs>
<data name="output" format="csv" label="${tool.name} on ${query}"/>
</outputs>
<tests>
<!-- Test basic search with known protein -->
<test>
<param name="query" value="P9WGR1"/>
<param name="index" value="chains"/>
<section name="filtering">
<param name="organism" value="Mycobacterium tuberculosis"/>
</section>
<output name="output" file="test-data/P9WGR1_basic.csv"/>
</test>
<!-- Test with TM-score sorting -->
<test>
<param name="query" value="Q9SBL1"/>
<param name="index" value="chains"/>
<section name="filtering">
<param name="organism" value="Mycobacterium tuberculosis"/>
</section>
<section name="sorting">
<param name="sort_by" value="tm_score"/>
<param name="sort_order" value="desc"/>
</section>
<output name="output" file="test-data/Q9SBL1_sorted.csv"/>
</test>
</tests>
<help><![CDATA[
**AlphaFind Protein Search**

This tool searches the AlphaFind API for structurally similar proteins based on 3D structural similarity.

-----

**What is AlphaFind?**

AlphaFind is a service for searching protein structures using AlphaFold predictions. It uses structural embeddings to find proteins with similar 3D conformations.

-----

**Input Parameters**

* **Protein Query**: A UniProt protein ID (e.g., P0A6F5, Q8Y547, Q9SBL1)

* **Search Index**: Choose which structural databases to search:
- *Chains*: Full protein chains (recommended)
- *Chains 90%*: Chains filtered to 90% sequence identity
- *Chains 80%*: Chains filtered to 80% sequence identity
- *Chains 70%*: Chains filtered to 70% sequence identity
- *Domains*: Protein domains (independent structural units)

* **Optional Filters**: Narrow your search results
- *Organism Name*: Filter by organism (e.g., 'Mycobacterium tuberculosis')
- *Taxonomy ID*: Filter by NCBI taxonomy ID (numeric)
- *Gene Name*: Filter by gene symbol
- *CATH Annotation*: Filter by CATH structural classification (domains only)

* **Search Options**:
- *Number of Similar Proteins*: Control result size (1-5000). Note that even with low k, the API may return all available matches up to 5000.
- *Timeout*: Maximum wait time for computations (60-3600 seconds). Complex searches may take several minutes.

* **Sorting**:
- *KNN Similarity*: Sort by embedding similarity score
- *TM-Score*: Sort by structural alignment TM-score

-----

**Output Format**

The tool produces a CSV file with 23 columns:

- query_id: Unique query identifier
- index_type: Index type used
- page_number: Page number (internal)
- target_id: Target protein ID
- score: KNN similarity score (0-1)
- organism: Target protein organism
- tax_id: Taxonomy ID
- gene_name: Gene symbol
- protein_name: Protein name
- avg_plddt: AlphaFold prediction quality
- tm_score_query: TM-score (query as reference)
- tm_score_target: TM-score (target as reference)
- rmsd: Root-mean-square deviation
- sequential_identity: Sequence alignment identity
- aligned_residues: Aligned residue ratio
- status: Computation status
- created_at: Computation start time
- completed_at: Computation end time
- has_experimental_structure: Experimental structure available
- pdb_ids: PDB identifiers
- chopping: Domain boundaries (if domains)
- tar_index: Internal reference

-----

**Important Notes**

* This is a web-based API. The tool requires internet connectivity to https://alphafind.ics.muni.cz
* Computations may take from seconds to several minutes depending on query complexity
* Results are cached by the API, so repeated queries may complete faster
* The API can return up to 5000 results even with a low k value
* TM-score > 0.5 indicates significant structural similarity
* TM-score > 0.8 indicates very high structural similarity

-----

**Examples**

1. **Basic search**: Query protein P0A6F5 with default settings

2. **Find similar proteins in specific organism**:

- Query: Q8Y547
- Organism: Mycobacterium tuberculosis

3. **Domain-level search**:

- Query: F8U1Q0
- Index: domains
- CATH annotation: 1.10.8.10

4. **High-confidence results**:

- Query: P9WGR1
- Sort by: TM-Score
- Sort order: Descending

-----

**References**

* AlphaFind API: https://alphafind.ics.muni.cz
* AlphaFold DB: https://alphafold.ebi.ac.uk
* TM-Score paper: Yang & Skolnick, 2004

-----

**Troubleshooting**

* **"Protein not found"**: The query ID may not exist in AlphaFold DB or lacks embedding vectors. Verify the UniProt ID.
* **Timeout exceeded**: Increase the timeout value in Search Options.
* **Empty results**: Your filters may be too restrictive, or no similar proteins exist with the specified criteria.
* **"Search failed"**: The API encountered an error. Try again or check the API status.
]]></help>
<citations>
<citation type="doi">10.1038/nature14539</citation>
</citations>
</tool>
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