# HG changeset patch
# User galaxyp
# Date 1710765298 0
# Node ID 17c7ab82bfbc2e5c5720d97edcad7ce5320cd68d
# Parent  b04960a7abf5190f5063a67ae709073c83ffd0c0
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit f66aa9a65aaf45ac4888ca26f5af661f73b46fdc

diff -r b04960a7abf5 -r 17c7ab82bfbc convert_mga.py
--- a/convert_mga.py	Wed Mar 21 17:15:25 2018 -0400
+++ b/convert_mga.py	Mon Mar 18 12:34:58 2024 +0000
@@ -35,7 +35,7 @@
             '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 @@
             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 -r b04960a7abf5 -r 17c7ab82bfbc metagene_annotator.xml
--- a/metagene_annotator.xml	Wed Mar 21 17:15:25 2018 -0400
+++ b/metagene_annotator.xml	Mon Mar 18 12:34:58 2024 +0000
@@ -1,8 +1,15 @@
-<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>
     <command detect_errors="exit_code"><![CDATA[
         #set $output_list = str($output_formats).split(',')
@@ -50,7 +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"/>
@@ -61,7 +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"/>