Mercurial > repos > sanbi-uwc > data_manager_shapeit2_reference
diff data_manager/shapeit_ref.xml @ 0:4f7004475124 draft default tip
planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
| author | sanbi-uwc |
|---|---|
| date | Tue, 18 Sep 2018 00:54:49 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/shapeit_ref.xml Tue Sep 18 00:54:49 2018 -0400 @@ -0,0 +1,34 @@ +<tool id="shapeit_reference_manager" name="SHAPEIT reference data path manager" tool_type="manage_data" version="0.0.8"> + <command detect_errors="exit_code"><![CDATA[ + python $__tool_directory__/shapeit_ref.py + '${value}' + '${name}' + '${path}' + '${reference_prefix}' + '${map_prefix}' + '${sample_prefix}' + '${output_file}' + ]]></command>> + <inputs> + <param name="value" type="text" label="Short key to identify this reference set (no spaces)" /> + <param name="name" type="text" label="Description of the reference data" /> + <param name="path" type="text" label="Filesystem path to directory containing this reference set" /> + <param name="reference_prefix" type="text" label="Filename prefix for the reference (.hap / .legend / .sample) files" /> + <param name="map_prefix" type="text" label="Filename prefix for map files in this reference set" /> + <param name="sample_prefix" type="text" label="Filename prefix for sample file for this reference set"> + </inputs> + <outputs> + <data name="output_file" format="data_manager_json" /> + </outputs> + <help><![CDATA[ + This data manager updates the *shapeit_ref* table with information about locally-maintained reference data + used by the SHAPEIT_ haplotype estimation (i.e. phasing) package. An example for the 1000 Genomes + dataset is available here_. + + .. _SHAPEIT: http://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html + .. _here: https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.html + ]]></help> + <citations> + <citation type="doi">10.1038/nmeth.1785</citation> + </citations> +</tool>