test for script run

bin/physcraper_run.py

@@ -154,7 +154,8 @@
                                         configfile = conf)
     sys.stdout.write("{} taxa in alignment and tree\n".format(len(scraper.data.aln)))
     scraper.data.write_files()
-    scraper.data.write_files(treepath = "before_otu_{}.tre".format(scraper.data.tag), alnpath = "before_otu_{}.aln".format(scraper.data.tag))
+    scraper.data.write_files(treefilename = "before_otu_{}.tre".format(scraper.data.tag),
+                             alnfilename = "before_otu_{}.aln".format(scraper.data.tag))
     scraper.data.write_labelled(filename="before_labelled_{}".format(scraper.data.tag), label='^ot:ottTaxonName')
     scraper.data.write_otus(schema="json")
 

tests/test_script_run.py

@@ -0,0 +1,9 @@
+import subprocess
+
+def test_physcraper_run_script():
+    subprocess.check_call(["physcraper_run.py", "-s", "ot_350", 
+                                                "-t", "Tr53297",
+                                                "-a", "docs/examples/ot_350Tr53297.aln",
+                                                "-as", "nexus",
+                                                "-no_est",
+                                                "-o", "tmp_ot350"])