Mercurial > repos > devteam > data_manager_bowtie2_index_builder

annotate data_manager/bowtie2_index_builder.xml @ 7:1c0f8e9d87c6 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_bowtie2_index_builder commit 9fa01fe96452d50646e066066b1e556ba4a75ced"
author iuc
date Mon, 06 Apr 2020 19:27:05 -0400
parents 847c9ef56a52
children 76672b83d42d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
847c9ef56a52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 12dc2dbca65c1e2e1cb51c163daf0fa251d84d8e"
iuc
parents: 5
diff changeset
1 <tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="@WRAPPER_VERSION@.1+galaxy1" profile="18.09">
0
9458af1ab90b Uploaded
devteam
parents:
diff changeset
2 <description>builder</description>
9458af1ab90b Uploaded
devteam
parents:
diff changeset
3 <requirements>
4
d1d5feb31804 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents: 3
diff changeset
4 <requirement type="package" version="@WRAPPER_VERSION@">bowtie2</requirement>
0
9458af1ab90b Uploaded
devteam
parents:
diff changeset
5 </requirements>
4
d1d5feb31804 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents: 3
diff changeset
6 <macros>
6
847c9ef56a52 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 12dc2dbca65c1e2e1cb51c163daf0fa251d84d8e"
iuc
parents: 5
diff changeset
7 <token name="@WRAPPER_VERSION@">2.3.5</token>
4
d1d5feb31804 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents: 3
diff changeset
8 </macros>
3
83da94c0e4a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 2
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
83da94c0e4a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 2
diff changeset
10 python '$__tool_directory__/bowtie2_index_builder.py'
83da94c0e4a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 2
diff changeset
11 '${out_file}'
83da94c0e4a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 2
diff changeset
12 --fasta_filename '${all_fasta_source.fields.path}'
83da94c0e4a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 2
diff changeset
13 --fasta_dbkey '${all_fasta_source.fields.dbkey}'
83da94c0e4a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 2
diff changeset
14 --fasta_description '${all_fasta_source.fields.name}'
83da94c0e4a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 2
diff changeset
15 --data_table_name bowtie2_indexes ${tophat2}
83da94c0e4a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 2
diff changeset
16 ]]></command>
0
9458af1ab90b Uploaded
devteam
parents:
diff changeset
17 <inputs>
9458af1ab90b Uploaded
devteam
parents:
diff changeset
18 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
9458af1ab90b Uploaded
devteam
parents:
diff changeset
19 <options from_data_table="all_fasta"/>
9458af1ab90b Uploaded
devteam
parents:
diff changeset
20 </param>
3
83da94c0e4a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 2
diff changeset
21 <param name="sequence_name" type="text" value="" label="Name of sequence" />
83da94c0e4a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 2
diff changeset
22 <param name="sequence_id" type="text" value="" label="ID for sequence" />
83da94c0e4a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 2
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
9458af1ab90b Uploaded
devteam
parents:
diff changeset
24 </inputs>
9458af1ab90b Uploaded
devteam
parents:
diff changeset
25 <outputs>
9458af1ab90b Uploaded
devteam
parents:
diff changeset
26 <data name="out_file" format="data_manager_json"/>
9458af1ab90b Uploaded
devteam
parents:
diff changeset
27 </outputs>
4
d1d5feb31804 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents: 3
diff changeset
28 <tests>
d1d5feb31804 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents: 3
diff changeset
29 <test>
d1d5feb31804 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents: 3
diff changeset
30 <param name="all_fasta_source" value="phiX174"/>
d1d5feb31804 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents: 3
diff changeset
31 <output name="out_file" value="bowtie2_data_manager.json"/>
d1d5feb31804 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents: 3
diff changeset
32 </test>
d1d5feb31804 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e
iuc
parents: 3
diff changeset
33 </tests>
0
9458af1ab90b Uploaded
devteam
parents:
diff changeset
34
9458af1ab90b Uploaded
devteam
parents:
diff changeset
35 <help>
9458af1ab90b Uploaded
devteam
parents:
diff changeset
36 .. class:: infomark
9458af1ab90b Uploaded
devteam
parents:
diff changeset
37
3
83da94c0e4a6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 2
diff changeset
38 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
0
9458af1ab90b Uploaded
devteam
parents:
diff changeset
39 </help>
9458af1ab90b Uploaded
devteam
parents:
diff changeset
40 </tool>