view chewbbaca_createschema.xml @ 13:35ee71a46436 draft

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<tool id="chewbbaca_createschema" name="chewBBACA CreateSchema" version="2.1.0+galaxy0">
    <description>Create a gene by gene schema based on genomes</description>
    <requirements>
        <requirement type="package" version="2.1.0">chewbbaca</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        mkdir assemblies &&
        ln -s
        #for $assembly in $assemblies:
          '${assembly}'
        #end for
        assemblies &&
        chewBBACA.py CreateSchema
          --cpu \${GALAXY_SLOTS:-1}
          -i assemblies
          #if str( $prodigal_training_file_source.prodigal_training_file_source_selector ) == 'tool_data_table':
            --ptf '${prodigal_training_file_source.prodigal_training_file.fields.path}'
          #elif str( $prodigal_training_file_source.prodigal_training_file_source_selector ) == 'history':
            --ptf '${prodigal_training_file_source.prodigal_training_file}'
          #end if
          #if $cds:
            --CDS '${cds}'
          #end if
          --bsr '${bsr}'
          -o schema
          && tar -czf schema.tgz schema
        ]]>
    </command>
    <inputs>
        <param name="assemblies" format="fasta" type="data_collection" collection_type="list" label="Assembled genomes (fasta)" />
        <conditional name="prodigal_training_file_source">
            <param name="prodigal_training_file_source_selector" type="select"
                   label="Select a Prodigal training file from your history or use one from a tool data table?">
                <option value="No" selected="true">No Prodigal training file</option>
                <option value="tool_data_table">Prodigal training file from tool data table</option>
                <option value="history">Prodigal training file from history</option>
            </param>
            <when value="No"/>
            <when value="tool_data_table">
                <param name="prodigal_training_file" type="select" format="tabular" label="Prodigal Training File">
                    <options from_data_table="prodigal_training_files">
                        <validator type="no_options" message="No prodigal training files are available" />
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="prodigal_training_file" type="data" format="binary"
                       label="Prodigal training file"
                       help=""/>
            </when>
        </conditional>
        <param name="bsr" type="float" value="0.6" optional="true" label="BSR score" />
        <param name="cds" type="data" format="fasta" optional="true" label="Coding sequence file for schema creation (fasta)" />
    </inputs>
    <outputs>
        <data name="schema" type="list" format="fasta" label="${tool.name}: on ${on_string}: Schema">
            <discover_datasets pattern="__name_and_ext__" format="fasta" directory="schema" />
        </data>
        <data name="schema_zipped" format="zip" label="${tool.name}: on ${on_string}: Schema (zipped)" from_work_dir="schema.tgz">
        </data>
    </outputs>
    <tests>
        <test>
            <param name="prodigal_training_file_source_selector" value="history" />
            <param name="prodigal_training_file" value="prodigal_training_files/Streptococcus_agalactiae.trn" />
            <param name="assemblies">
                <collection type="list">
                    <element name="assembly1" value="assemblies/GCA_000007265.1_ASM726v1_genomic_2kbases.fna" />
                    <element name="assembly2" value="assemblies/GCA_000012705.1_ASM1270v1_genomic_2kbases.fna" />
                </collection>
            </param>
            <output name="schema_zipped" file="test_1_schema.tgz" compare="sim_size" />
        </test>
        <test>
            <param name="prodigal_training_file_source_selector" value="tool_data_table" />
            <param name="prodigal_training_file" value="Streptococcus_agalactiae" />
            <param name="assemblies">
                <collection type="list">
                    <element name="assembly1" value="assemblies/GCA_000007265.1_ASM726v1_genomic_2kbases.fna" />
                    <element name="assembly2" value="assemblies/GCA_000012705.1_ASM1270v1_genomic_2kbases.fna" />
                </collection>
            </param>
            <output name="schema_zipped" file="test_1_schema.tgz" compare="sim_size" />
        </test>
    </tests>
    <help><![CDATA[
    ]]>
    </help>
   <expand macro="citations"/>
</tool>