Mercurial > repos > iuc > data_manager_build_kma_index
view data_manager/kma_build_index.xml @ 1:8c2e674a93bb draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit 848c47fb29e9f1d319056a94a7dbd90129a4aafc"
author | iuc |
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date | Tue, 07 Apr 2020 23:20:00 -0400 |
parents | 889cc43b72d6 |
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<?xml version="1.0"?> <tool id="kma_build_index" name="KMA Index Builder" tool_type="manage_data" version="1.2.21+galaxy0" profile="19.01"> <description>kma index builder</description> <requirements> <requirement type="package" version="1.2.21">kma</requirement> <requirement type="package" version="3.7">python</requirement> </requirements> <version_command>kma -v</version_command> <command detect_errors="exit_code"> <![CDATA[ python '${__tool_directory__}/kma_build_index.py' '${out_file}' --k ${k} --k_t ${k_t} --k_i ${k_i} --ML ${ML} --ht ${ht} --hq ${hq} --name '${name}' '${fasta}' ]]> </command> <inputs> <param name="k" type="integer" value="16" min="8" max="32" label="kmer size used for indexing the database." /> <param name="k_t" type="integer" value="16" min="8" max="32" label="kmer size used to identify template candidates when running KMA." /> <param name="k_i" type="integer" value="16" min="8" max="32" label="kmer size used when performing alignments between two sequences." /> <param name="ML" type="integer" value="16" label="Minimum length of templates" /> <param name="ht" type="float" value="1.0" min="0.0" max="1.0" label="Homology template" /> <param name="hq" type="float" value="1.0" min="0.0" max="1.0" label="Homology query" /> <param name="name" type="text" label="Name for index" /> <param name="fasta" type="data" format="fasta" label="Sequence to index (fasta)" /> </inputs> <outputs> <data name="out_file" format="data_manager_json" /> </outputs> <tests> <test> <param name="fasta" value="phiX174.fasta"/> <param name="name" value="index"/> <output name="out_file" value="kma_data_manager.json" compare="sim_size" /> </test> </tests> <help> </help> <citations> <citation type="doi">10.1186/s12859-018-2336-6</citation> </citations> </tool>