Mercurial > repos > devteam > tabular_to_fastq
changeset 5:e8ca9af08774 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/galaxy_sequence_utils/tabular_to_fastq commit d4ced60a941c4c4a2fe95de9c09a10086810b387"
| author | iuc |
|---|---|
| date | Wed, 19 Feb 2020 17:08:16 +0000 |
| parents | 1f75d46e55f5 |
| children | 82c4bc769ba8 |
| files | macros.xml tabular_to_fastq.py tabular_to_fastq.xml |
| diffstat | 3 files changed, 23 insertions(+), 9 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Feb 19 17:08:16 2020 +0000 @@ -0,0 +1,9 @@ +<macros> + <token name="@TOOL_VERSION@">1.1.5</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">galaxy_sequence_utils</requirement> + <yield/> + </requirements> + </xml>> +</macros>
--- a/tabular_to_fastq.py Fri Nov 01 13:22:35 2019 -0400 +++ b/tabular_to_fastq.py Wed Feb 19 17:08:16 2020 +0000 @@ -14,15 +14,14 @@ max_col = max(identifier_col, sequence_col, quality_col) num_reads = None skipped_lines = 0 - out = open(output_filename, 'w') - for num_reads, line in enumerate(open(input_filename)): - fields = line.rstrip('\n\r').split('\t') - if len(fields) > max_col: - out.write("@%s\n%s\n+\n%s\n" % (fields[identifier_col], fields[sequence_col], fields[quality_col])) - else: - skipped_lines += 1 + with open(output_filename, 'w') as out: + for num_reads, line in enumerate(open(input_filename)): + fields = line.rstrip('\n\r').split('\t') + if len(fields) > max_col: + out.write("@%s\n%s\n+\n%s\n" % (fields[identifier_col], fields[sequence_col], fields[quality_col])) + else: + skipped_lines += 1 - out.close() if num_reads is None: print("Input was empty.") else:
--- a/tabular_to_fastq.xml Fri Nov 01 13:22:35 2019 -0400 +++ b/tabular_to_fastq.xml Wed Feb 19 17:08:16 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="tabular_to_fastq" name="Tabular to FASTQ" version="1.1.1"> +<tool id="tabular_to_fastq" name="Tabular to FASTQ" version="@TOOL_VERSION@"> <description>converter</description> <edam_topics> <edam_topic>topic_0622</edam_topic> @@ -6,6 +6,12 @@ <edam_operations> <edam_operation>operation_3434</edam_operation> </edam_operations> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="3.7">python</requirement> + </requirements> <command><![CDATA[ python '$__tool_directory__/tabular_to_fastq.py' '$input_file' '$output_file' '$identifier' '$sequence' '$quality' ]]></command>