Mercurial > repos > galaxyp > metagene_annotator
changeset 1:17c7ab82bfbc draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/metagene_annotator commit f66aa9a65aaf45ac4888ca26f5af661f73b46fdc
| author | galaxyp |
|---|---|
| date | Mon, 18 Mar 2024 12:34:58 +0000 |
| parents | b04960a7abf5 |
| children | |
| files | convert_mga.py metagene_annotator.xml |
| diffstat | 2 files changed, 15 insertions(+), 8 deletions(-) [+] |
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--- 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')
--- 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"/>