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annotate data_manager/shapeit_ref.xml @ 1:52f0767fe68d draft

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planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit b42d6cc8358088a50bc4463367c740c1e9dc71d8
author sanbi-uwc
date Thu, 13 Sep 2018 06:25:32 -0400
parents f86c65c60056
children 495439e68fca
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52f0767fe68d planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit b42d6cc8358088a50bc4463367c740c1e9dc71d8
sanbi-uwc
parents: 0
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1 <tool id="shapeit_reference_manager" name="SHAPEIT reference data path manager" tool_type="manage_data" version="0.0.2">
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f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
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2 <command detect_errors="aggressive"><![CDATA[
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
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3 python $__tool_directory__/shapeit_ref.py
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
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4 '${key}'
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
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5 '${description}'
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
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6 '${path}'
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52f0767fe68d planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit b42d6cc8358088a50bc4463367c740c1e9dc71d8
sanbi-uwc
parents: 0
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7 '${reference_prefix}'
52f0767fe68d planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit b42d6cc8358088a50bc4463367c740c1e9dc71d8
sanbi-uwc
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8 '${map_prefix}'
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f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
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9 '${output_file}'
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
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10 ]]></command>>
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
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11 <inputs>
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
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12 <param name="key" type="text" label="Short key to identify this reference set (no spaces)" />
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
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13 <param name="description" type="text" label="Description of the reference data" />
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
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14 <param name="path" type="text" label="Filesystem path to directory containing this reference set" />
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52f0767fe68d planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit b42d6cc8358088a50bc4463367c740c1e9dc71d8
sanbi-uwc
parents: 0
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15 <param name="reference_prefix" type="text" label="Filename prefix for the reference (.hap / .legend / .sample) files" />
52f0767fe68d planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit b42d6cc8358088a50bc4463367c740c1e9dc71d8
sanbi-uwc
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16 <param name="map_prefix" type="text" label="Filename prefix for map files in this reference set" />
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f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
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17 </inputs>
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
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18 <outputs>
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
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19 <data name="output_file" format="data_manager_json" />
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
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20 </outputs>
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
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21 <help><![CDATA[
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
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22 This data manager updates the *shapeit_ref* table with information about locally-maintained reference data
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
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23 used by the SHAPEIT_ haplotype estimation (i.e. phasing) package. An example for the 1000 Genomes
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
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24 dataset is available here_.
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
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25
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
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26 .. _SHAPEIT: http://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
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27 .. _here: https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.html
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
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28 ]]></help>
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
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29 <citations>
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
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30 <citation type="doi">10.1038/nmeth.1785</citation>
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
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31 </citations>
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
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32 </tool>