Mercurial > repos > devteam > data_manager_bowtie2_index_builder
annotate data_manager/bowtie2_index_builder.xml @ 3:49331eedb1c5 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bowtie2_index_builder commit c54b039220cc3d1767a424b6ae76852d40e67437
| author | devteam |
|---|---|
| date | Mon, 16 Nov 2015 15:12:06 -0500 |
| parents | 8de13c28d92e |
| children | 8a892275932f |
| rev | line source |
|---|---|
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49331eedb1c5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bowtie2_index_builder commit c54b039220cc3d1767a424b6ae76852d40e67437
devteam
parents:
2
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1 <tool id="bowtie2_index_builder_data_manager" name="Bowtie2 index" tool_type="manage_data" version="2.2.6"> |
| 0 | 2 <description>builder</description> |
| 3 <requirements> | |
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49331eedb1c5
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_bowtie2_index_builder commit c54b039220cc3d1767a424b6ae76852d40e67437
devteam
parents:
2
diff
changeset
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4 <requirement type="package" version="2.2.6">bowtie2</requirement> |
| 0 | 5 </requirements> |
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8de13c28d92e
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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6 <command interpreter="python">bowtie2_index_builder.py "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}" --data_table_name "bowtie2_indexes" ${tophat2}</command> |
| 0 | 7 <stdio> |
| 8 <exit_code range=":-1" /> | |
| 9 <exit_code range="1:" /> | |
| 10 </stdio> | |
| 11 <inputs> | |
| 12 <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> | |
| 13 <options from_data_table="all_fasta"/> | |
| 14 </param> | |
| 15 <param type="text" name="sequence_name" value="" label="Name of sequence" /> | |
| 16 <param type="text" name="sequence_id" value="" label="ID for sequence" /> | |
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8de13c28d92e
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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changeset
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17 <param type="boolean" name="tophat2" label="Also make available for TopHat" checked="True" truevalue="--data_table_name tophat2_indexes" falsevalue="" help="Adds values to tophat2_indexes tool data table." /> |
| 0 | 18 </inputs> |
| 19 <outputs> | |
| 20 <data name="out_file" format="data_manager_json"/> | |
| 21 </outputs> | |
| 22 | |
| 23 <help> | |
| 24 | |
| 25 .. class:: infomark | |
| 26 | |
| 27 **Notice:** If you leave name, description, or id blank, it will be generated automatically. | |
| 28 | |
| 29 </help> | |
| 30 </tool> |