Mercurial > repos > devteam > data_manager_bowtie2_index_builder
annotate data_manager/bowtie2_index_builder.xml @ 6:bb050998cee2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
author | iuc |
---|---|
date | Thu, 09 May 2019 16:15:27 -0400 |
parents | 8a892275932f |
children | 224f1598642a |
rev | line source |
---|---|
6
bb050998cee2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents:
5
diff
changeset
|
1 <tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="@WRAPPER_VERSION@" profile="18.09"> |
0 | 2 <description>builder</description> |
3 <requirements> | |
6
bb050998cee2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents:
5
diff
changeset
|
4 <requirement type="package" version="@WRAPPER_VERSION@">bowtie2</requirement> |
0 | 5 </requirements> |
6
bb050998cee2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents:
5
diff
changeset
|
6 <macros> |
bb050998cee2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents:
5
diff
changeset
|
7 <token name="@WRAPPER_VERSION@">2.3.4.3</token> |
bb050998cee2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents:
5
diff
changeset
|
8 </macros> |
5
8a892275932f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
3
diff
changeset
|
9 <command detect_errors="exit_code"><![CDATA[ |
8a892275932f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
3
diff
changeset
|
10 python '$__tool_directory__/bowtie2_index_builder.py' |
8a892275932f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
3
diff
changeset
|
11 '${out_file}' |
8a892275932f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
3
diff
changeset
|
12 --fasta_filename '${all_fasta_source.fields.path}' |
8a892275932f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
3
diff
changeset
|
13 --fasta_dbkey '${all_fasta_source.fields.dbkey}' |
8a892275932f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
3
diff
changeset
|
14 --fasta_description '${all_fasta_source.fields.name}' |
8a892275932f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
3
diff
changeset
|
15 --data_table_name bowtie2_indexes ${tophat2} |
8a892275932f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
3
diff
changeset
|
16 ]]></command> |
0 | 17 <inputs> |
18 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> | |
19 <options from_data_table="all_fasta"/> | |
20 </param> | |
5
8a892275932f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
3
diff
changeset
|
21 <param name="sequence_name" type="text" value="" label="Name of sequence" /> |
8a892275932f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
3
diff
changeset
|
22 <param name="sequence_id" type="text" value="" label="ID for sequence" /> |
8a892275932f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
3
diff
changeset
|
23 <param name="tophat2" type="boolean" truevalue="--data_table_name tophat2_indexes" falsevalue="" checked="True" label="Also make available for TopHat" help="Adds values to tophat2_indexes tool data table" /> |
0 | 24 </inputs> |
25 <outputs> | |
26 <data name="out_file" format="data_manager_json"/> | |
27 </outputs> | |
6
bb050998cee2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents:
5
diff
changeset
|
28 <tests> |
bb050998cee2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents:
5
diff
changeset
|
29 <test> |
bb050998cee2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents:
5
diff
changeset
|
30 <param name="all_fasta_source" value="phiX174"/> |
bb050998cee2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents:
5
diff
changeset
|
31 <output name="out_file" value="bowtie2_data_manager.json"/> |
bb050998cee2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents:
5
diff
changeset
|
32 </test> |
bb050998cee2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents:
5
diff
changeset
|
33 </tests> |
0 | 34 |
35 <help> | |
36 .. class:: infomark | |
37 | |
5
8a892275932f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
3
diff
changeset
|
38 **Notice:** If you leave name, description, or id blank, it will be generated automatically. |
0 | 39 </help> |
40 </tool> |