Mercurial > repos > p.lucas > get_major_minor
changeset 0:eb1a6c778688 draft
Uploaded wrapper
| author | p.lucas |
|---|---|
| date | Tue, 11 Jun 2024 10:05:25 +0000 |
| parents | |
| children | 54d44429c585 |
| files | VCF_create_major_and_minor_reference_wrapper.xml |
| diffstat | 1 files changed, 37 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/VCF_create_major_and_minor_reference_wrapper.xml Tue Jun 11 10:05:25 2024 +0000 @@ -0,0 +1,37 @@ +<tool id="get_major_minor_sequence" name="Create major and minor sequence with lofreq result" version="1"> + <description> + From lofreq result and the reference sequence used in alignment get + the MAJOR and the MINOR sequence in fasta format. + Provide 2 output fasta file, one sequence in each file. + </description> + <requirements> + <requirement type="package" version="1.79">biopython</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command interpreter="python" detect_errors="exit_code"><![CDATA[ + VCF_create_major_and_minor_reference.py + -v "$lofreq_output" + -r "$reference_fasta" + -M "$output_major" + -m "$output_minor" + ]]></command> + <inputs> + <param name="lofreq_output" type="data" format="vcf" label="Lofreq output" help="Lofreq output file in vcf format."/> + <param name="reference_fasta" type="data" format="fasta" label="Reference file" help="Reference file used with lofreq"/> + </inputs> + <outputs> + <data format="fasta" name="output_major" label="${tool.name} on ${on_string}: MAJOR"/> + <data format="fasta" name="output_minor" label="${tool.name} on ${on_string}: MINOR"/> + </outputs> + <help> + <![CDATA[ + +Homemade script to create two references with lofreq output: + - one file with all MAJOR mutation + - one file with all MINOR mutation + + ]]> + </help> +</tool>