genomicVariations_postprocessing.xml

<tool id="beacon2_genomic_variations_postprocessing" name="Beacon2 genomicVariations postprocessing" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>add caseLevelData or variantLevelData to existing Beacon genomic variations</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements"/>
    <expand macro="creators"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>

    <command detect_errors="exit_code"><![CDATA[
@BEACON2_RUNTIME_SETUP@ &&
touch conf/__init__.py &&
cp '$conf_py' 'conf/conf.py' &&
ln -s '$input_csv' 'input.csv' &&
genomicVariations_postprocessing.py
    --input 'input.csv'
    --datasetId '${dataset_id}'
    > output.log 2>&1
    ]]></command>
    <environment_variables>
        <environment_variable name="PYTHONPATH">.:\$PYTHONPATH</environment_variable>
    </environment_variables>
    <!-- SINGLE <configfiles> SECTION -->
    <configfiles>
        <configfile name="conf_py"><![CDATA[
# Auto-generated by the Galaxy wrapper for Beacon2 CSV to BFF

csv_folder = '.'
output_docs_folder = '.'
entry_type = '${advanced.entry_type}'
only_process_reads_with_allele_frequency = ${advanced.only_process_reads_with_allele_frequency}
populations_by_allele_counts = ${advanced.populations_by_allele_counts}
reference_genome = '${advanced.reference_genome}'
datasetId = '${dataset_id}'
case_level_data = ${advanced.case_level_data}
exact_heterozygosity = ${advanced.exact_heterozygosity}
num_rows = ${advanced.num_rows}
verbosity = ${advanced.verbosity}

# Database connection
database_host = '${advanced.database.database_host}'
database_port = ${advanced.database.database_port}
database_name = '${advanced.database.database_name}'

# Credentials (exact same logic as your beacon2-import tool)
#set $db_auth_source = $__user__.extra_preferences.get('beacon2_account|db_auth_source', "")
#set $db_user = $__user__.extra_preferences.get('beacon2_account|db_user', "")
#set $db_password = $__user__.extra_preferences.get('beacon2_account|db_password', "")
#if $db_user == "" or $db_password == "" or $db_auth_source == "":
    #set $db_auth_source = "admin"
    #set $db_user = "root"
    #set $db_password = "example"
#end if

database_user = '$db_user'
database_password = '$db_password'
database_auth_source = '$db_auth_source'
        ]]></configfile>
    </configfiles>

    <inputs>
        <param name="input_csv" type="data" format="csv" label="genomicVariations CSV for postprocessing"/>
        <expand macro="dataset_id"/>
        <!-- Full advanced options (single source of truth, includes custom conf.py) -->
        <!-- entry_type is hard-coded above because this tool is single-purpose -->
        <expand macro="advanced_section"/>
    </inputs>

    <outputs>
        <expand macro="log_output"/>
    </outputs>

    <tests>
        <test>
            <param name="input_csv" value="genomicVariations.csv" />
            <param name="dataset_id" value="test_dataset" />
            <output name="log" compare="contains">
                <assert_contents>
                    <has_text text="Successfully updated" />
                </assert_contents>
            </output>
        </test>
    </tests>

    <help><![CDATA[
**Beacon2 genomicVariations Post-processing**

Adds `caseLevelData` or `variantLevelData` to genomic variations that have already been loaded into the Beacon MongoDB.

**New flexible options (Advanced section):**
- Reference genome
- Case-level data generation
- Maximum rows to process (0 = unlimited)
- Allele frequency & population settings
- Verbose logging
- **Custom conf.py** (upload your own optimized config file for full control)

MongoDB credentials are read automatically from your Galaxy user preferences.
    ]]></help>
    <expand macro="citations"/>
</tool>