galaxytools/tools/sylph/macros.xml at 5566c61d7bb1354f63a77f8613f4906913659acd · tcollins2011/galaxytools · GitHub

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<macros>
    <token name="@TOOL_VERSION@">0.6.1</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@LICENSE@">MIT</token>
    <token name="@DB_SELECTOR@"><![CDATA[
        #if $database_select.select == 'cached':
        ln -s '$database_select.sylph_database.fields.path/database.syldb' 'database.syldb' &&
        #else:
            ln -s '$database_select.sylph_database' 'database.syldb' &&
        #end if
    ]]></token>
    <token name="@SINGLE_INPUT@"><![CDATA[
        #if $sketch.input.ext == 'fastqsanger'
        #set $ext = 'fastq'
        #else if $sketch.input.ext == 'fastqsanger.gz':
            #set $ext = 'fastq.gz'
        #else:
            #set $ext = str($sketch.input.ext)
        #end if
        #if $sketch.input.element_identifier.endswith('.fastq') or $sketch.input.element_identifier.endswith('.fastq.gz'):
            #set $input = re.sub(r'\s+', '_', $sketch.input.element_identifier)
        #else:
            #set $input = re.sub(r'\s+', '_', $sketch.input.element_identifier + '.' + str($ext))
        #end if
        ln -s '$sketch.input' '$input' &&
    ]]></token>
    <token name="@SINGLE_GROUP@"><![CDATA[
        #set input = ''
        #for $number, $current_file in enumerate($sketch.input):
            #if $current_file.ext == 'fastqsanger'
                #set $ext = 'fastq'
            #else if $current_file.ext == 'fastqsanger.gz':
                #set $ext = 'fastq.gz'
            #else:
                #set $ext = str($current_file.ext)
            #end if
            #if $current_file.element_identifier.endswith('.fastq') or $current_file.element_identifier.endswith('.fastq.gz'):
                #set $current_input = re.sub(r'\s+', '_', $current_file.element_identifier)
            #else:
                #set $current_input = re.sub(r'\s+', '_', $current_file.element_identifier + '.' + str($ext))
            #end if
            ln -s '${current_file}' '$current_input' &&
            #set input = str($input) + ' ' + str($current_input)
        #end for
    ]]></token>
    <token name="@PAIRED@"><![CDATA[
        #if $sketch.input_1.ext == 'fastqsanger'
                #set $ext_1 = 'fastq'
            #else if $sketch.input_1.ext == 'fastqsanger.gz':
                #set $ext_1 = 'fastq.gz'
            #else:
                #set $ext_1 = str($sketch.input_1.ext)
            #end if

            #if $sketch.input_2.ext == 'fastqsanger'
                #set $ext_2 = 'fastq'
            #else if $sketch.input_2.ext == 'fastqsanger.gz':
                #set $ext_2 = 'fastq.gz'
            #else:
                #set $ext_2 = str($sketch.input_2.ext)
            #end if

            #if $sketch.input_1.element_identifier.endswith('.fastq') or $sketch.input_1.element_identifier.endswith('.fastq.gz'):
                #set $read1 = re.sub(r'\s+', '_', $sketch.input_1.element_identifier)
            #else:
                #set $read1 = re.sub(r'\s+', '_', str($sketch.input_1.element_identifier) + '.' + str($ext_1))
            #end if
            #if $sketch.input_2.element_identifier.endswith('.fastq') or $sketch.input_2.element_identifier.endswith('.fastq.gz'):
                #set $read2 = re.sub(r'\s+', '_', $sketch.input_2.element_identifier)
            #else:
                #set $read2 = re.sub(r'\s+', '_', str($sketch.input_2.element_identifier) + '.' + str($ext_2))
            #end if
            ln -s '$sketch.input_1' '$read1' &&
            ln -s '$sketch.input_2' '$read2' &&
    ]]></token>
    <token name="@PAIRED_GROUP@"><![CDATA[
        #if $sketch.input.forward.ext == 'fastqsanger'
            #set $ext_1 = 'fastq'
        #else if $sketch.input.forward.ext == 'fastqsanger.gz':
            #set $ext_1 = 'fastq.gz'
        #else:
            #set $ext_1 = str($sketch.input.forward.ext)
        #end if

        #if $sketch.input.reverse.ext == 'fastqsanger'
            #set $ext_2 = 'fastq'
        #else if $sketch.input.reverse.ext == 'fastqsanger.gz':
            #set $ext_2 = 'fastq.gz'
        #else:
            #set $ext_2 = str($sketch.input.reverse.ext)
        #end if

        #set $read1 = re.sub(r'\s+', '_', str($sketch.input.element_identifier) + '.' + str($ext_1))
        #set $read2 = re.sub(r'\s+', '_', str($sketch.input.element_identifier) + '_r2.' + str($ext_2))
        ln -s '$sketch.input.forward' '$read1' &&
        ln -s '$sketch.input.reverse' '$read2' &&
    ]]></token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">sylph</requirement>
            <requirement type="package" version="3.11.9">python</requirement>
            <requirement type="package" version="2.2.3">pandas</requirement>
        </requirements>
    </xml>
    <xml name="description">
        <description>fast and precise species-level metagenomic profiling with ANIs</description>
    </xml>
    <xml name="citation">
        <citations>
            <citation type="doi">10.1038/s41587-024-02412-y</citation>
        </citations>
    </xml>
    <xml name="creator">
        <creator>
            <organization name="University of Toronto" url="https://github.com/bluenote-1577/sylph"/>
        </creator>
    </xml>
    <xml name="xrefs">
        <xrefs>
            <xref type="bio.tools">sylph</xref>
        </xrefs>
    </xml>
    <xml name="input_database">
        <conditional name="database_select">
            <param name="select" type="select" label="Choose the source for databases and metadata">
                <option value="cached">Cached data</option>
                <option value="history">History</option>
            </param>
            <when value="cached">
                <param label="Select a sylph database" name="sylph_database" type="select">
                    <options from_data_table="sylph_databases">
                        <validator message="No Sylph databases are available" type="no_options" />
                    </options>
                </param>
            </when>
            <when value="history">
                <param label="Select a history dataset" name="sylph_database" type="data" format="binary" />
                <param label="Metadata file for metaphlan and krona outputs" name="metadata" type="data" format="tabular.gz" optional="true" help="The metata file MUST be directly associated with the input database. For more information, view the help text of the tool."/>
            </when>
        </conditional>
    </xml>
    <xml name="output_format">
        <param label="Additional output formats" name="outputs" type="select" display="checkboxes" multiple="true" help="In addition to Sylph's tabular output, you may ouput a file converted to these formats">
            <option value="metaphlan">Sylph's MetaPhlAn-like output</option>
            <option value="krona">Krona compatible</option>
        </param>
    </xml>
</macros>