Mercurial > repos > sanbi-uwc > assess_poliovirus_alignment
changeset 5:0e556a3f85d6 draft
planemo upload for repository https://github.com/pvanheus/polio_report commit a99e10fec2fac5aae70974c977eb3b362a1a8429-dirty
author | sanbi-uwc |
---|---|
date | Wed, 14 Sep 2022 09:21:44 +0000 |
parents | 1897677e107c |
children | ca5b3e9740b9 |
files | assess_alignment.py assess_poliovirus_alignment.xml |
diffstat | 2 files changed, 14 insertions(+), 3 deletions(-) [+] |
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--- a/assess_alignment.py Fri Jul 22 09:55:46 2022 +0000 +++ b/assess_alignment.py Wed Sep 14 09:21:44 2022 +0000 @@ -145,11 +145,13 @@ if __name__ == "__main__": parser = argparse.ArgumentParser() parser.add_argument("--output_filename", help="Path to output file") + parser.add_argument("--consensus_output_filename", help="Path to output file for best consensus") parser.add_argument("--sample_name", help="Name of sample being analysed") parser.add_argument( "--dataset_names", type=comma_split, help="Comma separated names for datasets" ) parser.add_argument("--datasets", nargs="+") + parser.add_argument("--consensi", nargs="+") args = parser.parse_args() offsets = { @@ -182,6 +184,7 @@ best_match_mismatch_list = mismatch_list best_match_quality = quality best_match_reference = dataset_name + best_consensus = args.consensi[file_index] percent_mismatches = round(min_mismatches / lengths[best_match_reference] * 100, 2) info = { @@ -190,6 +193,8 @@ "mismatches": min_mismatches, "mismatch_list": best_match_mismatch_list, "quality": best_match_quality, - "perc_mismatches": percent_mismatches + "perc_mismatches": percent_mismatches, } json.dump(info, open(args.output_filename, "w")) + + open(args.consensus_output_filename, "w").write(best_consensus)
--- a/assess_poliovirus_alignment.xml Fri Jul 22 09:55:46 2022 +0000 +++ b/assess_poliovirus_alignment.xml Wed Sep 14 09:21:44 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="assess_poliovirus_alignment" name="Assess poliovirus alignment" version="0.3.0+galaxy0" profile="21.05"> +<tool id="assess_poliovirus_alignment" name="Assess poliovirus alignment" version="0.4.0+galaxy0" profile="21.05"> <requirements> <requirement type="package" version="3.9">python</requirement> </requirements> @@ -7,11 +7,16 @@ python $__tool_directory__/assess_alignment.py --dataset_names '$dataset_names' --output_filename '$output1' + --consensus_output_filename '$output_consensus' --sample_name '$tracy_results.name' --datasets #for $dataset in $tracy_results '$dataset' #end for + --consensi + #for $consensus in $tracy_consensus_results + '$consensus' + #end for ]]></command> <inputs> @@ -20,9 +25,10 @@ </inputs> <outputs> <data name="output1" format="json" label="Poliovirus alignment assessment on ${on_string}" /> + <data name="output_consensus" format="fasta" label="Poliovirus best consensus on ${on_string}" /> </outputs> <tests> - <test expect_num_outputs="1"> + <test expect_num_outputs="2"> <param name="tracy_results" ftype="json"> <collection type="list"> <element name="poliovirus1sabin" value="sample1/poliovirus1sabin.json" />