Mercurial > repos > rhpvorderman > updio
changeset 0:0bc9750fc1db draft default tip
planemo upload commit 1b7d98a104f966bbc5edbbee79160b8994b57081
| author | rhpvorderman |
|---|---|
| date | Wed, 13 Dec 2023 15:41:00 +0000 |
| parents | |
| children | |
| files | updio.xml |
| diffstat | 1 files changed, 56 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/updio.xml Wed Dec 13 15:41:00 2023 +0000 @@ -0,0 +1,56 @@ +<tool id="updio" name="UPDio" version="1.1.0+galaxy3" python_template_version="3.5" profile="21.05"> + <requirements> + <requirement type="package" version="1.1.0">updio</requirement> + <container type="docker">quay.io/biocontainers/updio:1.1.0--hdfd78af_0</container> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #if str($input_type.input_type_selector) == "file" + #from pathlib import Path + #set $child_id = Path(str($input_type.child_id_file)).read_text().strip() + #set $mother_id = Path(str($input_type.mother_id_file)).read_text().strip() + #set $father_id = Path(str($input_type.father_id_file)).read_text().strip() + #end if + ln -s $multisample_vcf input.vcf.gz && + updio --multisample_vcf input.vcf.gz + --childID $child_id + --momID $mother_id + --dadID $father_id && + mv output_dir/${child_id}.table ${updio_table} && + mv output_dir/${child_id}.upd ${updio_verdict} + ]]></command> + <inputs> + <param name="multisample_vcf" type="data" format="vcf_bgzip" + label="multisample VCF file" /> + <param name="output_label" type="text" + label="Analysis name, to distinguish the output." /> + <conditional name="input_type"> + <param name="input_type_selector" type="select" label="Sample IDs submitted by:"> + <option value="text" selected="true">Text</option> + <option value="file">Files (for easier workflow integration)</option> + </param> + <when value="text"> + <param name="child_id" type="text" + label="child sample ID in the VCF file" /> + <param name="mother_id" type="text" + label="Mother sample ID in the VCF file" /> + <param name="father_id" type="text" + label="Father sample ID in the VCF file" /> + </when> + <when value="file"> + <param name="child_id_file" type="data" + label="Child sample ID in the VCF file. Provided as a single line file."/> + <param name="mother_id_file" type="data" + label="Mother sample ID in the VCF file. Provided as a single line file."/> + <param name="father_id_file" type="data" + label="Father sample ID in the VCF file. Provided as a single line file."/> + </when> + </conditional> + </inputs> + <outputs> + <data format="tsv" name="updio_table" label="${tool.name} on ${output_label}: table"/> + <data format="tsv" name="updio_verdict" label="${tool.name} on ${output_label}: verdict"/> + </outputs> + <help><![CDATA[ + UPDio is designed to detect UPD events in probands from vcf trio data. + ]]></help> +</tool> \ No newline at end of file