Mercurial > repos > sanbi-uwc > data_manager_shapeit2_reference

annotate data_manager/shapeit_ref.xml @ 0:4f7004475124 draft default tip

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 aa91508cbd163b7b005d87824ffa997e62d5add6
author sanbi-uwc
date Tue, 18 Sep 2018 00:54:49 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
1 <tool id="shapeit_reference_manager" name="SHAPEIT reference data path manager" tool_type="manage_data" version="0.0.8">
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
2 <command detect_errors="exit_code"><![CDATA[
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
3 python $__tool_directory__/shapeit_ref.py
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
4 '${value}'
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
5 '${name}'
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
6 '${path}'
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
7 '${reference_prefix}'
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
8 '${map_prefix}'
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
9 '${sample_prefix}'
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
10 '${output_file}'
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
11 ]]></command>>
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
12 <inputs>
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
13 <param name="value" type="text" label="Short key to identify this reference set (no spaces)" />
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
14 <param name="name" type="text" label="Description of the reference data" />
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
15 <param name="path" type="text" label="Filesystem path to directory containing this reference set" />
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
16 <param name="reference_prefix" type="text" label="Filename prefix for the reference (.hap / .legend / .sample) files" />
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
17 <param name="map_prefix" type="text" label="Filename prefix for map files in this reference set" />
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
18 <param name="sample_prefix" type="text" label="Filename prefix for sample file for this reference set">
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
19 </inputs>
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
20 <outputs>
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
21 <data name="output_file" format="data_manager_json" />
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
22 </outputs>
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
23 <help><![CDATA[
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
24 This data manager updates the *shapeit_ref* table with information about locally-maintained reference data
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
25 used by the SHAPEIT_ haplotype estimation (i.e. phasing) package. An example for the 1000 Genomes
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
26 dataset is available here_.
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
27
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
28 .. _SHAPEIT: http://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
29 .. _here: https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.html
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
30 ]]></help>
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
31 <citations>
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
32 <citation type="doi">10.1038/nmeth.1785</citation>
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
33 </citations>
4f7004475124 planemo upload for repository https://github.com/pvanheus/data_manager_shapeit_reference commit aa91508cbd163b7b005d87824ffa997e62d5add6
sanbi-uwc
parents:
diff changeset
34 </tool>