Mercurial > repos > sanbi-uwc > data_manager_shapeit_reference

annotate data_manager/shapeit_ref.xml @ 6:6b54dcb42cd5 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 c9772b96ea77a4daac91b5fc87643972a1d71eda-dirty
author sanbi-uwc
date Mon, 17 Sep 2018 06:04:44 -0400
parents f0c7cab2f547
children ec2c5e521533
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
6b54dcb42cd5 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9772b96ea77a4daac91b5fc87643972a1d71eda-dirty
sanbi-uwc
parents: 5
diff changeset
1 <tool id="shapeit_reference_manager" name="SHAPEIT reference data path manager" tool_type="manage_data" version="0.0.7">
5
f0c7cab2f547 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit 1e78071ffc35990e3ea5846a6cc07e194f886cf0
sanbi-uwc
parents: 4
diff changeset
2 <command detect_errors="exit_code"><![CDATA[
0
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
3 python $__tool_directory__/shapeit_ref.py
3
203133a92000 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit 74cb5dd2b3aaed4a5b26840b451b8f2920e4b9fe-dirty
sanbi-uwc
parents: 2
diff changeset
4 '${value}'
4
094bd0114876 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit 06f9376308b504cd2ab7a4ff0126ae70d73faacc
sanbi-uwc
parents: 3
diff changeset
5 '${name}'
0
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
6 '${path}'
1
52f0767fe68d planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit b42d6cc8358088a50bc4463367c740c1e9dc71d8
sanbi-uwc
parents: 0
diff changeset
7 '${reference_prefix}'
52f0767fe68d planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit b42d6cc8358088a50bc4463367c740c1e9dc71d8
sanbi-uwc
parents: 0
diff changeset
8 '${map_prefix}'
5
f0c7cab2f547 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit 1e78071ffc35990e3ea5846a6cc07e194f886cf0
sanbi-uwc
parents: 4
diff changeset
9 '${sample_prefix}'
0
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
10 '${output_file}'
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
11 ]]></command>>
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
12 <inputs>
3
203133a92000 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit 74cb5dd2b3aaed4a5b26840b451b8f2920e4b9fe-dirty
sanbi-uwc
parents: 2
diff changeset
13 <param name="value" type="text" label="Short key to identify this reference set (no spaces)" />
4
094bd0114876 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit 06f9376308b504cd2ab7a4ff0126ae70d73faacc
sanbi-uwc
parents: 3
diff changeset
14 <param name="name" type="text" label="Description of the reference data" />
0
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
15 <param name="path" type="text" label="Filesystem path to directory containing this reference set" />
1
52f0767fe68d planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit b42d6cc8358088a50bc4463367c740c1e9dc71d8
sanbi-uwc
parents: 0
diff changeset
16 <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
parents: 0
diff changeset
17 <param name="map_prefix" type="text" label="Filename prefix for map files in this reference set" />
5
f0c7cab2f547 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit 1e78071ffc35990e3ea5846a6cc07e194f886cf0
sanbi-uwc
parents: 4
diff changeset
18 <param name="sample_prefix" type="text" label="Filename prefix for sample file for this reference set">
0
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
19 </inputs>
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
20 <outputs>
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
21 <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
22 </outputs>
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
23 <help><![CDATA[
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
24 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
25 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
26 dataset is available here_.
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
27
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
28 .. _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
29 .. _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
30 ]]></help>
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
31 <citations>
f86c65c60056 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9acc04bcb85873e6eb78b4163d1a7daa2679f22
sanbi-uwc
parents:
diff changeset
32 <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
33 </citations>
6
6b54dcb42cd5 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit c9772b96ea77a4daac91b5fc87643972a1d71eda-dirty
sanbi-uwc
parents: 5
diff changeset
34 </tool>