Mercurial > repos > bebatut > convert_extract_sequence_file
changeset 1:158642ce204f draft default tip
planemo upload commit 0a1bbb0870f6b776175151d4bc818c5546731ca8-dirty
| author | bebatut |
|---|---|
| date | Thu, 28 Apr 2016 08:36:12 -0400 |
| parents | 01c2b74b3a21 |
| children | |
| files | convert_extract_sequence_file.py convert_extract_sequence_file.xml test-data/information_lenght_fasta_output.txt |
| diffstat | 3 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/convert_extract_sequence_file.py Tue Apr 26 08:18:18 2016 -0400 +++ b/convert_extract_sequence_file.py Thu Apr 28 08:36:12 2016 -0400 @@ -42,7 +42,7 @@ return None split_line = id_line[1:].split(' ') seq_id = split_line[0] - description = ' '.join(split_line[1:]) + description = id_line[1:] new_line = get_new_line(input_file, generate_error = False) seq = '' while new_line != None: @@ -265,7 +265,7 @@ if args.custom_extraction_type == 'True': to_extract = args.to_extract[1:-1].split(',') with open(args.output_information, 'w') as output_information_file: - output_information_file.write('\t'.join(to_extract) + '\n') + #output_information_file.write('\t'.join(to_extract) + '\n') for record in self.conserved_records: extracted_info = record.extract_information(to_extract) string_info = [str(info) for info in extracted_info]
--- a/convert_extract_sequence_file.xml Tue Apr 26 08:18:18 2016 -0400 +++ b/convert_extract_sequence_file.xml Thu Apr 28 08:36:12 2016 -0400 @@ -7,6 +7,7 @@ <param name="to_extract" type="select" display="checkboxes" multiple="true" label="Information to extract" help=""> <option value="id">Identifiant</option> <option value="length">Length</option> + <option value="description">Description</option> <validator type="no_options" message="Select at least one information to extract"/> </param> </xml> @@ -179,7 +180,7 @@ </inputs> <outputs> - <data format="txt" name="information_file" + <data format="tabular" name="information_file" label="${tool.name} on ${on_string}: Information"> <filter>((sequence_file_format['extraction']['specific_extraction'] == "True" ))</filter> </data>