Fix metageneannotator bio.tools (#745)

* Fix metageneannotator bio.tools * Fix linting * Try to fix python linting --------- Co-authored-by: Björn Grüning <bjoern.gruening@gmail.com>
galaxyproteomics · Mar 18, 2024 · f66aa9a · f66aa9a
1 parent c810d2e
commit f66aa9a
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Showing 3 changed files with 16 additions and 13 deletions.
diff --git a/tools/metagene_annotator/.shed.yml b/tools/metagene_annotator/.shed.yml
@@ -25,3 +25,4 @@ name: metagene_annotator
 owner: galaxyp
 remote_repository_url: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator
 type: unrestricted
+homepage_url: http://metagene.nig.ac.jp/
diff --git a/tools/metagene_annotator/convert_mga.py b/tools/metagene_annotator/convert_mga.py
@@ -35,7 +35,7 @@ def __main__():
             'complete/partial', 'gene score', 'used model',
             'rbs start', 'rbs end', 'rbs score']))
 
-    gc_rbs_pat = '# gc = (-?[0-9]*[.]?[0-9]+), rbs = (-?[0-9]*[.]?[0-9]+)' 
+    gc_rbs_pat = '# gc = (-?[0-9]*[.]?[0-9]+), rbs = (-?[0-9]*[.]?[0-9]+)'
     seq_count = 0
     gene_count = 0
     for i, line in enumerate(input_rdr):
@@ -46,12 +46,12 @@ def __main__():
             try:
                 m = re.match(gc_rbs_pat, line.strip())
                 seq_gc, seq_rbs = m.groups()
-            except:
+            except ValueError:
                 seq_gc = seq_rbs = ''
         elif line.startswith('# self:'):
             seq_type = re.sub('# self:', '', line.rstrip())
         elif line.startswith('# '):
-            seq_name = re.sub('# (\S+).*$', '\\1', line.rstrip())
+            seq_name = re.sub(r'# (\S+).*$', '\\1', line.rstrip())
             seq_count += 1
         else:
             fields = line.split('\t')

diff --git a/tools/metagene_annotator/metagene_annotator.xml b/tools/metagene_annotator/metagene_annotator.xml
@@ -1,14 +1,16 @@
-<tool id="metagene_annotator" name="MetaGeneAnnotator" version="1.0.0">
+<tool id="metagene_annotator" name="MetaGeneAnnotator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>gene-finding program for prokaryote and phage (used by sixgill)</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">metageneannotator</xref>
+    </xrefs>
     <requirements>
-        <requirement type="package">metagene_annotator</requirement>
-        <requirement type="package">python</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">metagene_annotator</requirement>
+        <requirement type="package" version="3.10">python</requirement>
     </requirements>
-    <xml name="biotools">
-        <xrefs>
-            <xref type="bio.tools">metageneannotator</xref>
-        </xrefs>
-    </xml>
     <command detect_errors="exit_code"><![CDATA[
         #set $output_list = str($output_formats).split(',')
         touch mga_output
@@ -55,7 +57,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="1">
             <param name="inputs" value="metasequences.fasta" ftype="fasta"/>
             <param name="multiple_species" value="True"/>
             <param name="output_formats" value="txt"/>
@@ -66,7 +68,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="inputs" value="metasequences.fasta" ftype="fasta"/>
             <param name="multiple_species" value="False"/>
             <param name="output_formats" value="txt"/>