use cancer type in CIViC results

docs/usage.rst

@@ -180,6 +180,7 @@ A typical command to query the `Clinical Interpretations of Variants in Cancer -
         -v input_file.vcf \
         -o outdir \
         -g ref_genome [GRCh37, GRCh38, NCBI36]
+        -d 'breast adenocarcinoma'
 
 The command above generates the following result files using `CIViCpy <https://docs.civicpy.org/>`_.
 
@@ -193,6 +194,8 @@ The querynator performs an ``exact`` search, meaning that variants in the KB mus
 
 Using the ``filter_vep`` `flag <https://querynator.readthedocs.io/en/latest/usage.html#filtering-benign-variants>`_, the querynator can filter out benign variants in ``vcf`` files before querying the KB.
 
+The cancer type must be a valid `Disease Ontology <https://disease-ontology.org/>`_ ID (DOID) or name.
+
 Input file format
 ==================
 

querynator/__main__.py

@@ -427,7 +427,14 @@ def query_api_cgi(mutations, cnas, translocations, cancer, genome, token, email,
     show_default=True,
     default=False,
 )
-def query_api_civic(vcf, outdir, genome, filter_vep):
+@click.option(
+    "-c",
+    "--cancer",
+    help="the cancer DOID (id or name) to be searched.",
+    default=None,
+    type=click.STRING,
+)
+def query_api_civic(vcf, outdir, genome, cancer_doid, filter_vep):
     try:
         result_dir = get_unique_querynator_dir(f"{outdir}")
         dirname, basename = os.path.split(result_dir)
@@ -440,7 +447,7 @@ def query_api_civic(vcf, outdir, genome, filter_vep):
 
             logger.info("Query the Clinical Interpretations of Variants In Cancer (CIViC)")
             # run analysis
-            query_civic(candidate_variants, result_dir, logger, vcf, genome, filter_vep)
+            query_civic(candidate_variants, result_dir, logger, vcf, genome, cancer_doid, filter_vep)
 
         else:
             logger.info("Query the Clinical Interpretations of Variants In Cancer (CIViC)")