Mercurial > repos > devteam > data_manager_rsync_g2

annotate data_manager/data_manager_rsync.xml @ 2:e0329ab30f6d 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/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
author iuc
date Thu, 28 Nov 2019 15:47:47 -0500
parents 8ff92bd7e2a3
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
e0329ab30f6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
iuc
parents: 1
diff changeset
1 <tool id="data_manager_rsync_g2" name="Rsync with g2" version="0.0.3" tool_type="manage_data" profile="19.05">
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
2 <options sanitize="False" />
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
3 <description>fetching</description>
2
e0329ab30f6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
iuc
parents: 1
diff changeset
4 <requirements>
e0329ab30f6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
iuc
parents: 1
diff changeset
5 <requirement type="package" version="3.7">python</requirement>
e0329ab30f6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
iuc
parents: 1
diff changeset
6 <requirement type="package" version="3.1.3">rsync</requirement>
e0329ab30f6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
iuc
parents: 1
diff changeset
7 </requirements>
1
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
9 python '$__tool_directory__/data_manager_rsync.py'
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
10 '${out_file}'
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
11 ]]></command>
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
12 <inputs>
2
e0329ab30f6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
iuc
parents: 1
diff changeset
13 <param name="dbkey" type="genomebuild" label="dbkey to search for Reference Data" help="Specify ? to show all" refresh_on_change="True"/>
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
14
2
e0329ab30f6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
iuc
parents: 1
diff changeset
15 <param name="data_table_names" type="select" display="checkboxes" multiple="True" optional="True" refresh_on_change="True"
1
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
16 label="Choose Desired Data Tables" dynamic_options="galaxy_code_get_available_data_tables( __trans__ )" />
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
17
2
e0329ab30f6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
iuc
parents: 1
diff changeset
18 <param name="data_table_entries" type="select" display="checkboxes" multiple="true" optional="false"
1
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
19 label="Choose Desired Data Tables Entries" dynamic_options="galaxy_code_get_available_data_tables_entries( __trans__, dbkey, data_table_names )" />
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
20 </inputs>
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
21 <outputs>
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
22 <data name="out_file" format="data_manager_json" dbkey="dbkey"/>
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
23 </outputs>
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
24 <tests>
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
25 <test>
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
26 <param name="dbkey" value="sacCer2"/>
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
27 <param name="data_table_names" value="all_fasta"/>
2
e0329ab30f6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
iuc
parents: 1
diff changeset
28 <param name="data_table_entries" value="eyJlbnRyeSI6IHsiZGJrZXkiOiAic2FjQ2VyMiIsICJuYW1lIjogIlllYXN0IChTYWNjaGFyb215Y2VzIGNlcmV2aXNpYWUpOiBzYWNDZXIyIiwgInBhdGgiOiAiL2N2bWZzL2RhdGEuZ2FsYXh5cHJvamVjdC5vcmcvYnloYW5kL3NhY0NlcjIvc2VxL3NhY0NlcjIuZmEiLCAidmFsdWUiOiAic2FjQ2VyMiJ9LCAibmFtZSI6ICJhbGxfZmFzdGEifQ=="/>
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
29 <output name="out_file" file="sacCer2_rsync_all_fasta.data_manager_json"/>
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
30 </test>
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
31 </tests>
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
32 <help>
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
33 **What it does**
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
34
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
35 This tool connects to the Galaxy Project's rsync reference data repository to download data and populate tool data tables.
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
36
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
37 ------
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
38
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
39 .. class:: infomark
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
40
1
8ff92bd7e2a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_rsync_g2 commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
41 **Notice:** If you do not have a particular data table defined, then it will be created and persisted dynamically.
0
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
42 </help>
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
43 <code file="data_manager_rsync.py" />
0a3a6f862104 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_rsync_g2 commit 704060ebdf7399ecce9e0e8bd7262727fe750c27-dirty
devteam
parents:
diff changeset
44 </tool>