comparison 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"

0:2af9137ba067

<?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>