Mercurial > repos > devteam > data_manager_picard_index_builder

annotate data_manager/picard_index_builder.xml @ 5:acaa6719a478 draft

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_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
author iuc
date Mon, 03 Feb 2020 22:27:13 +0000
parents 0663d25e619c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
acaa6719a478 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
parents: 3
diff changeset
1 <tool id="picard_index_builder_data_manager" name="Picard index" tool_type="manage_data" version="2.7.1+galaxy1" profile="18.09">
0
9a024421602a Uploaded
devteam
parents:
diff changeset
2 <description>builder</description>
9a024421602a Uploaded
devteam
parents:
diff changeset
3 <requirements>
3
0663d25e619c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
4 <requirement type="package" version="2.7.1">picard</requirement>
0
9a024421602a Uploaded
devteam
parents:
diff changeset
5 </requirements>
3
0663d25e619c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
6 <command detect_errors="exit_code"><![CDATA[
0663d25e619c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
7 python '$__tool_directory__/picard_index_builder.py'
0663d25e619c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
8 '${out_file}'
0663d25e619c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
9 --fasta_filename '${all_fasta_source.fields.path}'
0663d25e619c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
10 --fasta_dbkey '${all_fasta_source.fields.dbkey}'
0663d25e619c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
11 --fasta_description '${all_fasta_source.fields.name}'
0663d25e619c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
12 --data_table_name picard_indexes
0663d25e619c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
13 ]]></command>
0
9a024421602a Uploaded
devteam
parents:
diff changeset
14 <inputs>
9a024421602a Uploaded
devteam
parents:
diff changeset
15 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
9a024421602a Uploaded
devteam
parents:
diff changeset
16 <options from_data_table="all_fasta"/>
9a024421602a Uploaded
devteam
parents:
diff changeset
17 </param>
3
0663d25e619c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
18 <param name="sequence_name" type="text" value="" label="Name of sequence" />
0663d25e619c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
19 <param name="sequence_id" type="text" value="" label="ID for sequence" />
0
9a024421602a Uploaded
devteam
parents:
diff changeset
20 </inputs>
9a024421602a Uploaded
devteam
parents:
diff changeset
21 <outputs>
9a024421602a Uploaded
devteam
parents:
diff changeset
22 <data name="out_file" format="data_manager_json"/>
9a024421602a Uploaded
devteam
parents:
diff changeset
23 </outputs>
5
acaa6719a478 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
parents: 3
diff changeset
24 <tests>
acaa6719a478 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
parents: 3
diff changeset
25 <test>
acaa6719a478 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
parents: 3
diff changeset
26 <param name="all_fasta_source" value="phiX174"/>
acaa6719a478 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
parents: 3
diff changeset
27 <output name="out_file" value="picard_index_builder_data_manager.json"/>
acaa6719a478 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
parents: 3
diff changeset
28 </test>
acaa6719a478 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 31fc4022a8c2fef50a3aff9210091be21e8450ef"
iuc
parents: 3
diff changeset
29 </tests>
0
9a024421602a Uploaded
devteam
parents:
diff changeset
30 <help>
9a024421602a Uploaded
devteam
parents:
diff changeset
31 .. class:: infomark
9a024421602a Uploaded
devteam
parents:
diff changeset
32
3
0663d25e619c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_picard_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 0
diff changeset
33 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
0
9a024421602a Uploaded
devteam
parents:
diff changeset
34 </help>
9a024421602a Uploaded
devteam
parents:
diff changeset
35 </tool>