Mercurial > repos > devteam > data_manager_sam_fasta_index_builder
annotate data_manager/data_manager_sam_fasta_index_builder.xml @ 4:1865e693d8b2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 471c497769f0dbfa92ec1a91f4044062cb5f7a83-dirty
author | iuc |
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date | Thu, 14 Sep 2017 15:30:56 -0400 |
parents | 1f54e98616af |
children | cc4ef4d38cf9 |
rev | line source |
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1
cf875cbe2df4
Uploaded updated data manager that specifies samtools 0.1.19.
devteam
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0
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changeset
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1 <tool id="sam_fasta_index_builder" name="SAM FASTA index" tool_type="manage_data" version="0.0.2"> |
0 | 2 <description>builder</description> |
3 <requirements> | |
4
1865e693d8b2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 471c497769f0dbfa92ec1a91f4044062cb5f7a83-dirty
iuc
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3
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changeset
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4 <requirement type="package" version="1.5">samtools</requirement> |
0 | 5 </requirements> |
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1f54e98616af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
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1
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changeset
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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
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1
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changeset
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7 python '$__tool_directory__/data_manager_sam_fasta_index_builder.py' |
1f54e98616af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
1
diff
changeset
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8 '${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
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9 --fasta_filename '${all_fasta_source.fields.path}' |
1f54e98616af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
1
diff
changeset
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10 --fasta_dbkey '${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
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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
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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
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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> | |
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
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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
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19 <param name="sequence_id" type="text" value="" label="ID for sequence" /> |
0 | 20 </inputs> |
21 <outputs> | |
22 <data name="out_file" format="data_manager_json"/> | |
23 </outputs> | |
24 | |
25 <help> | |
26 .. class:: infomark | |
27 | |
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
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28 **Notice:** If you leave name, description, or id blank, it will be generated automatically. |
0 | 29 </help> |
30 </tool> |