annotate macro_output.xml @ 23:2891385d6ace draft default tip

planemo upload for repository https://github.com/usegalaxy-au/tools-au commit b347c6ccc82b14fcbff360b3357050d1d43e3ef5-dirty

<macros>
    <xml name="output_pdb_models">
        <data name="model5" format="pdb" from_work_dir="output/alphafold/ranked_4.pdb" label="${tool.name} on ${on_string}: PDB ranked 4">
            <filter>advanced['limit_model_outputs'] > 4</filter>
            <filter>not advanced['exit_after_msa']</filter>
        </data>
        <data name="model4" format="pdb" from_work_dir="output/alphafold/ranked_3.pdb" label="${tool.name} on ${on_string}: PDB ranked 3">
            <filter>advanced['limit_model_outputs'] > 3</filter>
            <filter>not advanced['exit_after_msa']</filter>
        </data>
        <data name="model3" format="pdb" from_work_dir="output/alphafold/ranked_2.pdb" label="${tool.name} on ${on_string}: PDB ranked 2">
            <filter>advanced['limit_model_outputs'] > 2</filter>
            <filter>not advanced['exit_after_msa']</filter>
        </data>
        <data name="model2" format="pdb" from_work_dir="output/alphafold/ranked_1.pdb" label="${tool.name} on ${on_string}: PDB ranked 1">
            <filter>advanced['limit_model_outputs'] > 1</filter>
            <filter>not advanced['exit_after_msa']</filter>
        </data>
        <data name="model1" format="pdb" from_work_dir="output/alphafold/ranked_0.pdb" label="${tool.name} on ${on_string}: PDB ranked 0">
            <filter>not advanced['exit_after_msa']</filter>
        </data>
    </xml>

    <xml name="output_pae_csv">
        <data
            name="pae_ranked_4"
            format="csv"
            from_work_dir="output/alphafold/extra/pae_ranked_4.csv"
            label="${tool.name} on ${on_string}: pae_ranked_4.csv"
        >
            <filter>outputs['pae_csv']</filter>
            <filter>model_preset != "monomer"</filter>
            <filter>advanced['limit_model_outputs'] > 4</filter>
            <filter>not advanced['exit_after_msa']</filter>
        </data>
        <data
            name="pae_ranked_3"
            format="csv"
            from_work_dir="output/alphafold/extra/pae_ranked_3.csv"
            label="${tool.name} on ${on_string}: pae_ranked_3.csv"
        >
            <filter>outputs['pae_csv']</filter>
            <filter>model_preset != "monomer"</filter>
            <filter>advanced['limit_model_outputs'] > 3</filter>
            <filter>not advanced['exit_after_msa']</filter>
        </data>
        <data
            name="pae_ranked_2"
            format="csv"
            from_work_dir="output/alphafold/extra/pae_ranked_2.csv"
            label="${tool.name} on ${on_string}: pae_ranked_2.csv"
        >
            <filter>outputs['pae_csv']</filter>
            <filter>model_preset != "monomer"</filter>
            <filter>advanced['limit_model_outputs'] > 2</filter>
            <filter>not advanced['exit_after_msa']</filter>
        </data>
        <data
            name="pae_ranked_1"
            format="csv"
            from_work_dir="output/alphafold/extra/pae_ranked_1.csv"
            label="${tool.name} on ${on_string}: pae_ranked_1.csv"
        >
            <filter>outputs['pae_csv']</filter>
            <filter>model_preset != "monomer"</filter>
            <filter>advanced['limit_model_outputs'] > 1</filter>
            <filter>not advanced['exit_after_msa']</filter>
        </data>
        <data
            name="pae_ranked_0"
            format="csv"
            from_work_dir="output/alphafold/extra/pae_ranked_0.csv"
            label="${tool.name} on ${on_string}: pae_ranked_0.csv"
        >
            <filter>outputs['pae_csv']</filter>
            <filter>model_preset != "monomer"</filter>
            <filter>not advanced['exit_after_msa']</filter>
        </data>
    </xml>

    <xml name="output_pickles">
        <data
            name="output_ranked_4_pkl"
            format="binary"
            from_work_dir="output/alphafold/extra/ranked_4.pkl"
            label="${tool.name} on ${on_string}: ranked_4.pkl"
        >
            <filter>outputs['model_pkls']</filter>
            <filter>advanced['limit_model_outputs'] > 4</filter>
            <filter>not advanced['exit_after_msa']</filter>
        </data>
        <data
            name="output_ranked_3_pkl"
            format="binary"
            from_work_dir="output/alphafold/extra/ranked_3.pkl"
            label="${tool.name} on ${on_string}: ranked_3.pkl"
        >
            <filter>outputs['model_pkls']</filter>
            <filter>advanced['limit_model_outputs'] > 3</filter>
            <filter>not advanced['exit_after_msa']</filter>
        </data>
        <data
            name="output_ranked_2_pkl"
            format="binary"
            from_work_dir="output/alphafold/extra/ranked_2.pkl"
            label="${tool.name} on ${on_string}: ranked_2.pkl"
        >
            <filter>outputs['model_pkls']</filter>
            <filter>advanced['limit_model_outputs'] > 2</filter>
            <filter>not advanced['exit_after_msa']</filter>
        </data>
        <data
            name="output_ranked_1_pkl"
            format="binary"
            from_work_dir="output/alphafold/extra/ranked_1.pkl"
            label="${tool.name} on ${on_string}: ranked_1.pkl"
        >
            <filter>outputs['model_pkls']</filter>
            <filter>advanced['limit_model_outputs'] > 1</filter>
            <filter>not advanced['exit_after_msa']</filter>
        </data>
        <data
            name="output_ranked_0_pkl"
            format="binary"
            from_work_dir="output/alphafold/extra/ranked_0.pkl"
            label="${tool.name} on ${on_string}: ranked_0.pkl"
        >
            <filter>outputs['model_pkls']</filter>
            <filter>not advanced['exit_after_msa']</filter>
        </data>
    </xml>

    <xml name="output_plots">
        <data
            name="plot_ranked_4"
            format="png"
            from_work_dir="output/alphafold/extra/ranked_4.png"
            label="${tool.name} on ${on_string}: pLDDT/PAE plot ranked 4"
        >
            <filter>outputs['plots']</filter>
            <filter>advanced['limit_model_outputs'] > 4</filter>
            <filter>not advanced['exit_after_msa']</filter>
        </data>
        <data
            name="plot_ranked_3"
            format="png"
            from_work_dir="output/alphafold/extra/ranked_3.png"
            label="${tool.name} on ${on_string}: pLDDT/PAE plot ranked 3"
        >
            <filter>outputs['plots']</filter>
            <filter>advanced['limit_model_outputs'] > 3</filter>
            <filter>not advanced['exit_after_msa']</filter>
        </data>
        <data
            name="plot_ranked_2"
            format="png"
            from_work_dir="output/alphafold/extra/ranked_2.png"
            label="${tool.name} on ${on_string}: pLDDT/PAE plot ranked 2"
        >
            <filter>outputs['plots']</filter>
            <filter>advanced['limit_model_outputs'] > 2</filter>
            <filter>not advanced['exit_after_msa']</filter>
        </data>
        <data
            name="plot_ranked_1"
            format="png"
            from_work_dir="output/alphafold/extra/ranked_1.png"
            label="${tool.name} on ${on_string}: pLDDT/PAE plot ranked 1"
        >
            <filter>outputs['plots']</filter>
            <filter>advanced['limit_model_outputs'] > 1</filter>
            <filter>not advanced['exit_after_msa']</filter>
        </data>
        <data
            name="plot_ranked_0"
            format="png"
            from_work_dir="output/alphafold/extra/ranked_0.png"
            label="${tool.name} on ${on_string}: pLDDT/PAE plot ranked 0"
        >
            <filter>outputs['plots']</filter>
            <filter>not advanced['exit_after_msa']</filter>
        </data>
    </xml>

    <xml name="output_confidence_scores">
        <data
            name="output_confidence_scores"
            format="tabular"
            from_work_dir="output/alphafold/extra/model_confidence_scores.tsv"
            label="${tool.name} on ${on_string}: Model confidence scores"
        >
            <filter>outputs['confidence_scores']</filter>
            <filter>not advanced['exit_after_msa']</filter>
        </data>
    </xml>

    <xml name="output_msa_plot">
        <data
            name="output_msa_plot"
            format="png"
            from_work_dir="output/alphafold/extra/msa_coverage.png"
            label="${tool.name} on ${on_string}: MSA plot"
        >
            <filter>outputs['plot_msa']</filter>
            <filter>not advanced['exit_after_msa']</filter>
        </data>
    </xml>

    <xml name="output_plddts">
        <data
            name="output_plddts"
            format="tabular"
            from_work_dir="output/alphafold/extra/plddts.tsv"
            label="${tool.name} on ${on_string}: Per-residue confidence scores (plddts)"
        >
            <filter>outputs['plddts']</filter>
            <filter>not advanced['exit_after_msa']</filter>
        </data>
    </xml>

    <xml name="output_relax_json">
        <data
            name="output_relax_json"
            format="json"
            from_work_dir="output/alphafold/extra/relax_metrics_ranked.json"
            label="${tool.name} on ${on_string}: relax_metrics_ranked.json"
        >
            <filter>outputs['relax_json']</filter>
            <filter>not advanced['exit_after_msa']</filter>
        </data>
    </xml>

    <xml name="output_timings_json">
        <data
            name="output_timings_json"
            format="json"
            from_work_dir="output/alphafold/timings.json"
            label="${tool.name} on ${on_string}: timings.json"
        >
            <filter>outputs['timings_json']</filter>
            <filter>not advanced['exit_after_msa']</filter>
        </data>
    </xml>

    <xml name="output_msa">
        <collection name="output_msa" type="list" label="${tool.name} on ${on_string}: MSAs">
            <discover_datasets
                pattern="__designation_and_ext__"
                directory="output/alphafold/extra/msas"
                format="zip"
                visible="false"
            />
            <filter>outputs['msa'] or advanced['exit_after_msa']</filter>
        </collection>
    </xml>
</macros>