Fix metadata bug (replicate)

Author: RJMW

dimspy/tools.py

@@ -209,8 +209,9 @@ def replicate_filter(source, ppm, replicates, min_peaks, rsd_thres=None, filelis
             pl.tags.add_tag("_".join(map(str, reps)), "replicates")
 
             for t in pls_comb[0].tags.tags:
-                if not pl.tags.has_tag_type(t.ttype):
-                    pl.tags.add_tag(t)
+                if t.ttype != "replicate":
+                    if not pl.tags.has_tag_type(t.ttype):
+                        pl.tags.add_tag(t)
 
             pl_filt = filter_attr(pl.copy(), attr_name="present", min_threshold=replicates, flag_name="pres_rsd")
             median_rsd = np.median(pl_filt.get_attribute("rsd", flagged_only=True))

tests/data/MTBLS79_subset/MTBLS79_mzml_peak_matrix_rf.hdf5

@@ -0,0 +1,4 @@
+filename	injectionOrder	replicates	batch	classLabel
+batch04_B02_rep01_301_2_302_3_303	1	1_2_3	1	blank
+batch04_QC17_rep01_262_2_263_3_264	4	1_2_3	1	QC
+batch04_S01_rep01_247_2_248_3_249	7	1_2_3	1	sample

tests/data/MTBLS79_subset/MTBLS79_mzml_triplicates_rf.hdf5

@@ -254,3 +254,9 @@ def test_create_sample_list(self):
         with open(to_test_result("filelist_csl_MTBLS79_mzml_peak_matrix.txt"), "rU") as test_result:
             with open(to_test_data("filelist_csl_MTBLS79_mzml_peak_matrix.txt"), "rU") as comp:
                 self.assertEqual(test_result.read(), comp.read())
+
+        pm = load_peaklists_from_hdf5(to_test_data("MTBLS79_mzml_triplicates_rf.hdf5"))
+        create_sample_list(pm, to_test_result("filelist_csl_MTBLS79_mzml_triplicates_rf.txt"))
+        with open(to_test_result("filelist_csl_MTBLS79_mzml_triplicates_rf.txt"), "rU") as test_result:
+            with open(to_test_data("filelist_csl_MTBLS79_mzml_triplicates_rf.txt"), "rU") as comp:
+                self.assertEqual(test_result.read(), comp.read())