Mercurial > repos > devteam > data_manager_bwa_mem_index_builder
annotate data_manager/bwa_mem_index_builder.xml @ 5:46066df8813d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
author | iuc |
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date | Tue, 04 Apr 2017 18:07:04 -0400 |
parents | 414a92a973fa |
children | 2a386b2383a1 |
rev | line source |
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414a92a973fa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_mem_index_builder commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
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changeset
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1 <tool id="bwa_mem_index_builder_data_manager" name="BWA-MEM index" tool_type="manage_data" version="0.0.3"> |
0 | 2 <description>builder</description> |
3 <requirements> | |
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414a92a973fa
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bwa_mem_index_builder commit ddee21fa767f3234a4e5a9acfeeabdded32e7d01
devteam
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3
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changeset
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4 <requirement type="package" version="0.7.15">bwa</requirement> |
0 | 5 </requirements> |
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46066df8813d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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4
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6 <command detect_errors="exit_code"><![CDATA[ |
46066df8813d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
4
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7 python '$__tool_directory__/bwa_mem_index_builder.py' |
46066df8813d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
4
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changeset
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8 '${out_file}' |
46066df8813d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
4
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changeset
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9 --fasta_filename '${all_fasta_source.fields.path}' |
46066df8813d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
4
diff
changeset
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10 --fasta_dbkey '${all_fasta_source.fields.dbkey}' |
46066df8813d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
4
diff
changeset
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11 --fasta_description '${all_fasta_source.fields.name}' |
46066df8813d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
4
diff
changeset
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12 --data_table_name bwa_mem_indexes |
46066df8813d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
4
diff
changeset
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13 ]]></command> |
0 | 14 <inputs> |
15 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> | |
16 <options from_data_table="all_fasta"/> | |
17 </param> | |
5
46066df8813d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
4
diff
changeset
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18 <param name="sequence_name" type="text" value="" label="Name of sequence" /> |
46066df8813d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
4
diff
changeset
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19 <param name="sequence_id" type="text" value="" label="ID for sequence" /> |
46066df8813d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
4
diff
changeset
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20 |
0 | 21 <param name="index_algorithm" type="select" label="Algorithm for constructing BWT index"> |
5
46066df8813d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
4
diff
changeset
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22 <option value="automatic" selected="true">Guess automatically (2GB cut-off)</option> |
46066df8813d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
4
diff
changeset
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23 <option value="is">IS linear-time algorithm (for small genomes)</option> |
46066df8813d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
4
diff
changeset
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24 <option value="bwtsw">BWT-SW (for large genomes)</option> |
0 | 25 </param> |
26 </inputs> | |
27 <outputs> | |
28 <data name="out_file" format="data_manager_json"/> | |
29 </outputs> | |
30 | |
31 <help> | |
32 .. class:: infomark | |
33 | |
5
46066df8813d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bwa_mem_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
4
diff
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34 **Notice:** If you leave name, description, or id blank, it will be generated automatically. |
0 | 35 </help> |
36 </tool> |