Mercurial > repos > iuc > data_manager_salmon_index_builder
view data_manager/salmon_index_builder.xml @ 0:7d4fd734b078 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
author | iuc |
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date | Wed, 24 Jul 2019 07:17:00 -0400 |
parents | |
children | 6b0f2bdcc1b7 |
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<tool id="salmon_index_builder_data_manager" name="Salmon" tool_type="manage_data" version="0.11.3" profile_version="19.01"> <description>index builder</description> <requirements> <requirement type="package" version="0.11.3">salmon</requirement> <requirement type="package" version="3.7">python</requirement> </requirements> <macros> <token name="@IDX_VERSION@">q5</token> </macros> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/salmon_index_builder.py' --output '${out_file}' --fasta_filename '${all_fasta_source.fields.path}' --fasta_dbkey '${all_fasta_source.fields.dbkey}' --fasta_description '${all_fasta_source.fields.name}' --kmer_size "${kmer_size}" --data_table_name salmon_indexes_versioned --index_version @IDX_VERSION@ ]]> </command> <inputs> <param label="Source FASTA Sequence" name="all_fasta_source" type="select"> <options from_data_table="all_fasta" /> </param> <param name="sequence_name" type="text" value="" label="Name of sequence" /> <param name="sequence_id" type="text" value="" label="ID for sequence" /> <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" 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 "/> </inputs> <outputs> <data name="out_file" format="data_manager_json" /> </outputs> <tests> <test> <param name="all_fasta_source" value="phiX174"/> <param name="sequence_name" value="sequence_name"/> <param name="sequence_id" value="sequence_id"/> <output name="out_file" file="salmon_phiX174.data_manager_json"/> </test> </tests> <help> <![CDATA[ .. class:: infomark **Notice:** If you leave name, description, or id blank, it will be generated automatically. ]]> </help> <citations> <citation type="doi">https://doi.org/10.1038/nmeth.4197</citation> </citations> </tool>