Mercurial > repos > ieguinoa > data_manager_salmon_index_builder
comparison data_manager/salmon_index_builder.xml @ 1:c5dea2080109 draft
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| author | ieguinoa |
|---|---|
| date | Tue, 14 Aug 2018 11:19:49 -0400 |
| parents | |
| children | d22f69a2e80e |
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| 0:6cd60ba8a842 | 1:c5dea2080109 |
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| 1 <tool id="salmon_index_builder_data_manager" name="Salmon" tool_type="manage_data" version="0.9.1"> | |
| 2 <description>index builder</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.9.1">salmon</requirement> | |
| 5 </requirements> | |
| 6 <command detect_errors="exit_code"><![CDATA[ | |
| 7 python '$__tool_directory__/salmon_index_builder.py' --output '${out_file}' | |
| 8 --fasta_filename '${all_fasta_source.fields.path}' | |
| 9 --fasta_dbkey '${all_fasta_source.fields.dbkey}' | |
| 10 --fasta_description '${all_fasta_source.fields.name}' | |
| 11 --kmer_size "${kmer_size}" | |
| 12 --data_table_name salmon_indexes | |
| 13 ]]> | |
| 14 </command> | |
| 15 <inputs> | |
| 16 <param label="Source FASTA Sequence" name="all_fasta_source" type="select"> | |
| 17 <options from_data_table="all_fasta" /> | |
| 18 </param> | |
| 19 <param name="sequence_name" type="text" value="" label="Name of sequence" /> | |
| 20 <param name="sequence_id" type="text" value="" label="ID for sequence" /> | |
| 21 <param name="kmer_size" type="integer" optional='true' value="21" max="32" label="The size of the k-mer on which the index is built" | |
| 22 help="There is a tradeoff here between the distinctiveness of the k-mers and their robustness to errors. The shorter the k-mers, the more robust they will be to errors in the reads, but the longer the k-mers, the more distinct they will be. We generally recommend using a k-mer size of at least 20. MUST BE AN ODD VALUE "/> | |
| 23 | |
| 24 | |
| 25 | |
| 26 </inputs> | |
| 27 <outputs> | |
| 28 <data name="out_file" format="data_manager_json" /> | |
| 29 </outputs> | |
| 30 <help> | |
| 31 <![CDATA[ | |
| 32 .. class:: infomark | |
| 33 | |
| 34 **Notice:** If you leave name, description, or id blank, it will be generated automatically. | |
| 35 ]]> | |
| 36 </help> | |
| 37 </tool> | |
| 38 |