galaxy-tool-BLAST/blastn.xml at master · naturalis/galaxy-tool-BLAST · GitHub

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<tool id="blastn" name="Identify reads with blastn and find taxonomy" version="1.5">
    <!-- description>blastn wrapper and taxonomy finder</description-->
    <requirements>
        <requirement type="package" version="3.12.0">python</requirement>
        <requirement type="package" version="1.85">biopython</requirement>
        <requirement type="package" version="2.17.0">blast</requirement>
    </requirements>
    <command>
        <![CDATA[
        bash '$__tool_directory__/blastn.sh'
        $input_type.type
        $input_type.input
        #if $database_type.type == "local"
        $database_type.database.fields.path
        #elif $database_type.type == "user"
        $database_type.database
        #end if
        $task
        $max_target_seqs
        $output_format.output_format_type
        $log_output
        #if $input_type.type == "fasta"
        $blast_output_fasta
        #elif $input_type.type == "zip"
        $blast_output_zip
        #end if
        #if $output_format.output_format_type == "custom_taxonomy"
        $output_format.taxonomy_method
        $output_format.coverage
        #else
        "none"
        "none"
        #end if
        $identity
        $blast_output_original
        $database_type.type
        ]]>
    </command>
    <macros>
        <macro name="zip_file_input_macro">
            <param format="zip" name="input" type="data" label="zip file containing fasta"/>
        </macro>
        <macro name="fasta_file_input_macro">
            <param format="fasta" name="input" type="data" label="fasta file"/>
        </macro>
        <macro name="taxonomy_macro">
            <param name="taxonomy_method" type="select" multiple="false" label="Taxonomy source">
                <option value="none">None</option>
                <option value="default" selected="true">Taxonomy of the database from the hit</option>
                <option value="GBIF" selected="true">GBIF or Catalogue of Life (GBIF highest priority)</option>
            </param>
            <param name="coverage" type="float" label="Query Coverage percentage cutoff"  value="80" min="0.0" max="100"/>
        </macro>
        <macro name="local_databases">
        <param name="database" type="select" multiple="true" label="Database">
          <options from_data_table="naturalis_blast_databases">
             <validator message="No BLAST database is available" type="no_options" />
          </options>
        </param>
        </macro>
        <macro name="user_input_fasta">
            <param format="fasta" name="database" type="data" label="fasta file"/>
        </macro>

    </macros>
    <inputs>
        <conditional name="input_type">
            <param name="type" type="select" multiple="false" label="Input type">
                <option value="zip">zip</option>
                <option value="fasta" selected="true">fasta</option>
            </param>
            <when value="zip">
                <expand macro="zip_file_input_macro"/>
            </when>
            <when value="fasta">
                <expand macro="fasta_file_input_macro"/>
            </when>
        </conditional>
        <conditional name="database_type">
            <param name="type" type="select" multiple="false" label="Subject database/sequences">
                <option value="local" selected="true">Locally installed BLAST database</option>
                <option value="user">FASTA file from your history</option>
            </param>
            <when value="local">
                <expand macro="local_databases"/>
            </when>
            <when value="user">
                <expand macro="user_input_fasta"/>
            </when>
        </conditional>


        <!--<param name="taxidlist" type="select" multiple="false" label="NCBI taxonomy filter" dynamic_options="taxon_filter(database)"/>-->

        <param name="task" type="select" multiple="false" label="Task">
            <option value="blastn">blastn</option>
            <option value="megablast" selected="true">megablast</option>
        </param>

        <conditional name="output_format">
            <param name="output_format_type" type="select" multiple="false" label="Output format">
                <option value="custom_taxonomy" selected="true">With taxonomy (Default)</option>
                <option value="0">Pairwise (can be used with MEGAN)</option>
                <option value="6">Tabular</option>
                <option value="8">Text ASN.1</option>
                <option value="11">BLAST archive format (ASN.1)</option>
            </param>
            <when value="custom_taxonomy">
                <expand macro="taxonomy_macro"/>
            </when>
        </conditional>
        <param name="identity" type="float" label="Identity percentage cutoff"  value="97" min="0.0" max="100"/>
        <param name="max_target_seqs" type="integer" label="Maximum number of BLAST hits per sequence" value="1" min="1"/>

    </inputs>
    <!--<code file="/home/ubuntu/testmapMarten/test/Marten/github_scripts/galaxy-tool-BLAST/test_tool_form_utils.py"/>-->

    <outputs>
        <data format="txt" name="log_output" label="$input_type.input.display_name log"/>
        <!--<data format="tabular" name="blast_output" label="$input_type.input.display_name BLAST" />-->
        <data format="zip" name="blast_output_zip" label="$input_type.input.display_name BLAST">
            <filter>input_type['type'] != "fasta"</filter>
        </data>

        <!-- Output with original taxonomy -->
        <data format="tabular" name="blast_output_original" label="$input_type.input.display_name BLAST gbif taxonomy">
            <filter>input_type['type'] == "fasta"</filter>
            <filter>output_format['taxonomy_method'] == "GBIF"</filter>
        </data>

        <data format="tabular" name="blast_output_fasta" label="$input_type.input.display_name BLAST original taxonomy">
            <filter>input_type['type'] == "fasta"</filter>
            <change_format>
                <when input="output_format.output_format_type" value="custom_taxonomy" format="tabular"/>
                <when input="output_format.output_format_type" value="6" format="tabular"/>
                <when input="output_format.output_format_type" value="8" format="txt"/>
                <when input="output_format.output_format_type" value="0" format="txt"/>
                <when input="output_format.output_format_type" value="11" format="txt"/>
            </change_format>
        </data>
        <!-- tests upload changes -->

    </outputs>
    <!-- <tests>
        <test>
            <param name="test_input" value="test_input.txt"/>
            <output name="test_outout" file="test_output.txt"/>
        </test>
    </tests> -->
    <help>
    </help>
</tool>