Mercurial > repos > iuc > data_manager_mash_sketch_builder
diff data_manager/mash_sketch_builder.xml @ 0:2af9137ba067 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mash_sketch_builder/ commit c6efcbece52dec310253537b35419839746fff7f"
author | iuc |
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date | Wed, 26 Feb 2020 17:06:21 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/mash_sketch_builder.xml Wed Feb 26 17:06:21 2020 -0500 @@ -0,0 +1,74 @@ +<?xml version="1.0"?> +<tool id="mash_sketch_builder" name="Mash Sketch" tool_type="manage_data" version="@TOOL_VERSION@+galaxy0" profile="18.09"> + <description>builder</description> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">mash</requirement> + <requirement type="package" version="3.7">python</requirement> + </requirements> + <macros> + <token name="@TOOL_VERSION@">2.1</token> + </macros> + <version_command>mash --version</version_command> + <command detect_errors="exit_code"> + <![CDATA[ + python '$__tool_directory__/mash_sketch_builder.py' + '${out_file}' + --threads \${GALAXY_SLOTS:-1} + #if str( $input_sequence_source.input_sequence_source_selector ) == "tool_data_table": + --fasta '${input_sequence_source.input_sequence.fields.path}' + #elif str( $input_sequence_source.input_sequence_source_selector ) == 'history': + --fasta '${input_sequence_source.input_sequence}' + #end if + --sketch-name '${sketch_name}' + --sketch-size '${sketch_size}' + --kmer-size '${kmer_size}' + --probability-threshold '${probability_threshold}' + ${individual_sequences} + ]]> + </command> + <inputs> + <conditional name="input_sequence_source"> + <param name="input_sequence_source_selector" type="select" + label="Select a sequence from your history or use one from a tool data table?"> + <option value="tool_data_table">Sequence from tool data table</option> + <option selected="True" value="history">Sequence from history</option> + </param> + <when value="tool_data_table"> + <param name="input_sequence" type="select" label="Source FASTA Sequence"> + <options from_data_table="all_fasta"/> + </param> + </when> + <when value="history"> + <param name="input_sequence" type="data" format="fasta" label="Input sequence" help=""/> + </when> + </conditional> + <param type="text" name="sketch_name" label="Sketch name" help="Human-readable description of the sketch"/> + <param type="integer" name="sketch_size" value="1000" min="10" max="1000000" label="Sketch size" help="Each sketch will have at most this many non-redundant min-hashes."/> + <param type="integer" name="kmer_size" value="21" min="1" max="32" label="K-mer size" help="Hashes will be based on strings of this many nucleotides."/> + <param type="float" name="probability_threshold" value="0.01" min="0." max="1." label="Probability threshold for warning about low k-mer size." /> + <param type="boolean" name="individual_sequences" truevalue="--individual-sequences" falsevalue="" label="Sketch individual sequences" help="e.g. for multi-fastas of single-chromosome genomes or pair-wise gene comparisons."/> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" /> + </outputs> + <tests> + <test> + <param name="input_sequence_source_selector" value="history"/> + <param name="input_sequence" value="test_assembly.fasta"/> + <param name="sketch_name" value="Test Sketch" /> + <output name="out_file" value="mash_sketch_data_manager.json" compare="sim_size" /> + </test> + </tests> + <help><![CDATA[ + +**What it does** + + Create a sketch file, which is a reduced representation of a sequence or set + of sequences (based on min-hashes) that can be used for fast distance + estimations. For output, one sketch file will be generated, but it can have + multiple sketches within it, divided by sequences or files. + ]]></help> + <citations> + <citation type="doi">10.1186/s13059-016-0997-x</citation> + </citations> +</tool>