Mercurial > repos > devteam > data_manager_sam_fasta_index_builder

annotate data_manager/data_manager_sam_fasta_index_builder.xml @ 5:cc4ef4d38cf9 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_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
author iuc
date Mon, 18 Nov 2019 15:07:34 -0500
parents 1865e693d8b2
children f8418a1bf7d0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
cc4ef4d38cf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents: 4
diff changeset
1 <tool id="sam_fasta_index_builder" name="SAM FASTA index" tool_type="manage_data" version="0.0.3" profile="19.05">
0
d6b6db69d9bf Uploaded data manager definition.
devteam
parents:
diff changeset
2 <description>builder</description>
d6b6db69d9bf Uploaded data manager definition.
devteam
parents:
diff changeset
3 <requirements>
5
cc4ef4d38cf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents: 4
diff changeset
4 <requirement type="package" version="1.9">samtools</requirement>
0
d6b6db69d9bf Uploaded data manager definition.
devteam
parents:
diff changeset
5 </requirements>
3
1f54e98616af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 1
diff changeset
6 <command detect_errors="exit_code"><![CDATA[
1f54e98616af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 1
diff changeset
7 python '$__tool_directory__/data_manager_sam_fasta_index_builder.py'
1f54e98616af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 1
diff changeset
8 '${out_file}'
1f54e98616af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 1
diff changeset
9 --fasta_filename '${all_fasta_source.fields.path}'
1f54e98616af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 1
diff changeset
10 --fasta_dbkey '${all_fasta_source.fields.dbkey}'
1f54e98616af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 1
diff changeset
11 --fasta_description '${all_fasta_source.fields.name}'
1f54e98616af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 1
diff changeset
12 --data_table_name fasta_indexes
1f54e98616af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 1
diff changeset
13 ]]></command>
0
d6b6db69d9bf Uploaded data manager definition.
devteam
parents:
diff changeset
14 <inputs>
d6b6db69d9bf Uploaded data manager definition.
devteam
parents:
diff changeset
15 <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
d6b6db69d9bf Uploaded data manager definition.
devteam
parents:
diff changeset
16 <options from_data_table="all_fasta"/>
d6b6db69d9bf Uploaded data manager definition.
devteam
parents:
diff changeset
17 </param>
3
1f54e98616af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 1
diff changeset
18 <param name="sequence_name" type="text" value="" label="Name of sequence" />
1f54e98616af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 1
diff changeset
19 <param name="sequence_id" type="text" value="" label="ID for sequence" />
0
d6b6db69d9bf Uploaded data manager definition.
devteam
parents:
diff changeset
20 </inputs>
d6b6db69d9bf Uploaded data manager definition.
devteam
parents:
diff changeset
21 <outputs>
d6b6db69d9bf Uploaded data manager definition.
devteam
parents:
diff changeset
22 <data name="out_file" format="data_manager_json"/>
d6b6db69d9bf Uploaded data manager definition.
devteam
parents:
diff changeset
23 </outputs>
5
cc4ef4d38cf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents: 4
diff changeset
24 <tests>
cc4ef4d38cf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents: 4
diff changeset
25 <test>
cc4ef4d38cf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents: 4
diff changeset
26 <param name="all_fasta_source" value="phiX174"/>
cc4ef4d38cf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents: 4
diff changeset
27 <output name="out_file" value="sam_fasta_data_manager.json"/>"
cc4ef4d38cf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents: 4
diff changeset
28 </test>
cc4ef4d38cf9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 72fb3d356a87d2b555572486e7901449c3bdb568"
iuc
parents: 4
diff changeset
29 </tests>
0
d6b6db69d9bf Uploaded data manager definition.
devteam
parents:
diff changeset
30
d6b6db69d9bf Uploaded data manager definition.
devteam
parents:
diff changeset
31 <help>
d6b6db69d9bf Uploaded data manager definition.
devteam
parents:
diff changeset
32 .. class:: infomark
d6b6db69d9bf Uploaded data manager definition.
devteam
parents:
diff changeset
33
3
1f54e98616af planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents: 1
diff changeset
34 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
0
d6b6db69d9bf Uploaded data manager definition.
devteam
parents:
diff changeset
35 </help>
d6b6db69d9bf Uploaded data manager definition.
devteam
parents:
diff changeset
36 </tool>