Mercurial > repos > sanbi-uwc > data_manager_shapeit_reference

annotate data_manager/shapeit_ref.xml @ 0:f86c65c60056 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
author sanbi-uwc
date Tue, 11 Sep 2018 10:39:38 -0400
parents
children 52f0767fe68d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
1 <tool id="shapeit_reference_manager" name="SHAPEIT reference data path manager" tool_type="manage_data" version="0.0.1">
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
2 <command detect_errors="aggressive"><![CDATA[
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
3 python $__tool_directory__/shapeit_ref.py
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
4 '${key}'
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
5 '${description}'
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
6 '${path}'
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
7 '${prefix}'
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
8 '${output_file}'
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
9 ]]></command>>
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
10 <inputs>
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
11 <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
parents:
diff changeset
12 <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
parents:
diff changeset
13 <param name="path" type="text" label="Filesystem path to directory containing this reference set" />
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
14 <param name="prefix" type="text" label="Filename prefix for files in this reference set" />
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
15 </inputs>
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
16 <outputs>
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
17 <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
parents:
diff changeset
18 </outputs>
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
19 <help><![CDATA[
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
20 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
sanbi-uwc
parents:
diff changeset
21 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
sanbi-uwc
parents:
diff changeset
22 dataset is available here_.
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
23
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
24 .. _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
sanbi-uwc
parents:
diff changeset
25 .. _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
sanbi-uwc
parents:
diff changeset
26 ]]></help>
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
27 <citations>
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
28 <citation type="doi">10.1038/nmeth.1785</citation>
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
29 </citations>
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
30 </tool>