Mercurial > repos > devteam > data_manager_sam_fasta_index_builder
annotate data_manager/data_manager_sam_fasta_index_builder.xml @ 8:3ec5c51384e6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 20381ede5940c6bbca00b550e01550f5aad0f2b7"
author | iuc |
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date | Mon, 01 Nov 2021 08:32:15 +0000 |
parents | f8418a1bf7d0 |
children | a256278e5bff |
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8
3ec5c51384e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 20381ede5940c6bbca00b550e01550f5aad0f2b7"
iuc
parents:
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1 <tool id="sam_fasta_index_builder" name="SAM FASTA index" tool_type="manage_data" version="0.0.5" profile="19.05"> |
0 | 2 <description>builder</description> |
3 <requirements> | |
8
3ec5c51384e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 20381ede5940c6bbca00b550e01550f5aad0f2b7"
iuc
parents:
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4 <requirement type="package" version="1.14">samtools</requirement> |
6
f8418a1bf7d0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
iuc
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5 <requirement type="package" version="3.7">python</requirement> |
0 | 6 </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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7 <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
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changeset
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8 python '$__tool_directory__/data_manager_sam_fasta_index_builder.py' |
1f54e98616af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
1
diff
changeset
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9 '${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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10 --fasta_filename '${all_fasta_source.fields.path}' |
1f54e98616af
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sam_fasta_index_builder commit 8652f36a3a3838dca989426961561e81432acf4f
iuc
parents:
1
diff
changeset
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11 --fasta_dbkey '${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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12 --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
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changeset
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13 --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
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changeset
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14 ]]></command> |
0 | 15 <inputs> |
16 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> | |
17 <options from_data_table="all_fasta"/> | |
18 </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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19 <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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20 <param name="sequence_id" type="text" value="" label="ID for sequence" /> |
0 | 21 </inputs> |
22 <outputs> | |
23 <data name="out_file" format="data_manager_json"/> | |
24 </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:
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changeset
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25 <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
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changeset
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26 <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
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27 <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
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28 <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
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29 </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
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30 </tests> |
0 | 31 |
32 <help> | |
33 .. class:: infomark | |
34 | |
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
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changeset
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35 **Notice:** If you leave name, description, or id blank, it will be generated automatically. |
0 | 36 </help> |
37 </tool> |