# HG changeset patch
# User galaxyp
# Date 1610745059 0
# Node ID a475c1906e0b70bddcbfa28a1a7e7580a2483a1a
# Parent  84e4b5d4b7adfbddebf45f6b960a1c9a652de8a4
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyteomics commit 58fe8232b7f4659b37e8725197d63e81efae0683"

diff -r 84e4b5d4b7ad -r a475c1906e0b mztab2tsv.xml
--- a/mztab2tsv.xml	Fri Jan 15 15:58:54 2021 +0000
+++ b/mztab2tsv.xml	Fri Jan 15 21:10:59 2021 +0000
@@ -60,13 +60,13 @@
                 <assert_contents><has_text text="accession"/></assert_contents>
             </output>
             <output name="out_pep" ftype="tabular">
-                <assert_contents><has_text text="&quot;&quot;"/></assert_contents>
+                <assert_contents><has_n_lines n="0"/></assert_contents>
             </output>
             <output name="out_psm" ftype="tabular">
                 <assert_contents><has_text text="PSM_ID"/></assert_contents>
             </output>
             <output name="out_sml" ftype="tabular">
-                <assert_contents><has_text text="&quot;&quot;"/></assert_contents>
+                <assert_contents><has_n_lines n="0"/></assert_contents>
             </output>
         </test>
         <test expect_num_outputs="4">
diff -r 84e4b5d4b7ad -r a475c1906e0b mztab_reader.py
--- a/mztab_reader.py	Fri Jan 15 15:58:54 2021 +0000
+++ b/mztab_reader.py	Fri Jan 15 21:10:59 2021 +0000
@@ -9,43 +9,17 @@
 
 def read_mztab(input_path, output_path):
     """
-    Read mztab file
+    Read and process mztab file
     """
     mztab = MzTab(input_path)
-    if mztab.variant == 'P':
-        return read_mztab_p(mztab, output_path)
-    elif mztab.variant == 'M':
-        return read_mztab_m(mztab, output_path)
-
-
-def read_mztab_p(mztab, output_path):
-    """
-    Processing mztab "P"
-    """
     mtd = pd.DataFrame.from_dict(mztab.metadata, orient='index')
     mtd.to_csv(os.path.join(output_path, "mtd.tsv"), sep="\t")
-    prt = mztab.protein_table
-    prt.to_csv(os.path.join(output_path, "prt.tsv"), sep="\t")
-    pep = mztab.peptide_table
-    pep.to_csv(os.path.join(output_path, "pep.tsv"), sep="\t")
-    psm = mztab.spectrum_match_table
-    psm.to_csv(os.path.join(output_path, "psm.tsv"), sep="\t")
-    sml = mztab.small_molecule_table
-    sml.to_csv(os.path.join(output_path, "sml.tsv"), sep="\t")
-
-
-def read_mztab_m(mztab, output_path):
-    """
-    Processing mztab "M"
-    """
-    mtd = pd.DataFrame.from_dict(mztab.metadata, orient='index')
-    mtd.to_csv(os.path.join(output_path, "mtd.tsv"), sep="\t")
-    sml = mztab.small_molecule_table
-    sml.to_csv(os.path.join(output_path, "sml.tsv"), sep="\t")
-    smf = mztab.small_molecule_feature_table
-    smf.to_csv(os.path.join(output_path, "smf.tsv"), sep="\t")
-    sme = mztab.small_molecule_evidence_table
-    sme.to_csv(os.path.join(output_path, "sme.tsv"), sep="\t")
+    for name, tab in mztab:
+        if not tab.empty:
+            tab.to_csv(os.path.join(output_path, f"{name.lower()}.tsv"), sep="\t")
+        else:
+            with open(os.path.join(output_path, f"{name.lower()}.tsv"), "w"):
+                pass
 
 
 if __name__ == "__main__":