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Inputs
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The tool requires a path to a ro-crate (directory) passed in ``--inputdir`` parameter as its input.
The directory should contain following files:

- ``ppi_edgelist.tsv``
    A processed edge list file which represents protein-protein interactions, where proteins are identified by their symbols.

.. code-block::

    geneA	geneB
    DNMT3A	SAP18
    DNMT3A	DDX3X
    DNMT3A	SEC16A
    DNMT3A	U2SURP
    DNMT3A	SYNJ2

- ``ppi_gene_node_attributes.tsv``
    Contains attributes for each gene node in the protein-protein interaction network. This includes information like gene names, ensembl ID, and other relevant data.

    The code directly references only ``name`` column, which is required but also other columns may be present:

    * name - contains the gene symbol. In some cases, it can contain an ensembl ID or another query, that mygene was queried with.
    * represents - a comma-separated list of Ensembl gene IDs that the gene symbol represents.
    * ambiguous - a comma-separated list of gene symbols that are considered ambiguous.
    * bait - the bait column contains Boolean values (TRUE or FALSE) indicating whether the gene is considered a "bait" in the context of affinity purification mass spectrometry (APMS) experiments. Baits are proteins of interest that are used to pull down interacting partners (preys) from a cell extract. A value of TRUE suggests that the gene is used as a bait in such experiments, as determined by its presence in a provided bait_set.

.. code-block::

    name	represents	ambiguous	bait
    DNMT3A	ensembl:ENSG00000119772		TRUE
    HDAC2	ensembl:ENSG00000196591		TRUE
    KDM6A	ensembl:ENSG00000147050		TRUE
    SMARCA4	ensembl:ENSG00000127616		TRUE

- ``ro-crate-metadata.json``
    Metadata in RO-Crate format, a community effort to establish a lightweight approach to packaging research data with their metadata.

    The main object contains identifier (@id), type (@type), name, descriptions, keywords and isPartOf, that describes the hierarchical relationship (organization and project).

    Graph: The @graph key contains an array of objects that detail other entities related to the main dataset.
    a. Metadata, Datasets, Software
    b. Output Files: details of output files generated by the tool.