annotate macros.xml @ 0:24431ccf6352 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4

<macros>
    <token name="@TOOL_VERSION@">1.0</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">25.0</token>

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">amas</requirement>
        </requirements>
    </xml>

    <xml name="version_command">
        <version_command>python -c "import amas; print(amas.__version__)"</version_command>
    </xml>

    <token name="@SNIFF_INPUT_FORMAT@"><![CDATA[
        #set $in_format = $input_files[0].ext
        #if $in_format == 'nex'
            #set $in_format = 'nexus'
        #end if
    ]]></token>

    <token name="@CHECK_INTERLEAVED@"><![CDATA[
        ## Check if inputs are interleaved
        IN_FORMAT=\$(python '$__tool_directory__/check_interleaved.py' 
            #for $f in $input_files
                '${f}'
            #end for
            --format '${in_format}') &&
    ]]></token>

    <token name="@SYMLINK_INPUTS@"><![CDATA[
        ## Create symlinks with original filename for consistent tests
        #for $f in $input_files
            #set $safename_input = re.sub('[^\w\-_\.]', '_', $f.element_identifier)
            ln -s '${f}' '${safename_input}';
        #end for
    ]]></token>

    <token name="@INPUT_FILENAMES@"><![CDATA[
        #for $f in $input_files
            #set $safename_input = re.sub('[^\w\-_\.]', '_', $f.element_identifier)
            '${safename_input}'
        #end for
    ]]></token>

    <xml name="output_format" token_name="out_format" token_label="Format of the output file">
        <param name="out_format" type="select" label="@LABEL@">
            <option value="fasta">fasta</option>
            <option value="phylip">phylip (sequential)</option>
            <option value="phylip-int">phylip (interleaved)</option>
            <option value="nexus">nexus (sequential)</option>
            <option value="nexus-int">nexus (interleaved)</option>
        </param>
    </xml>

    <xml name="data_type">
        <param name="data_type" type="select" label="Data type">
            <option value="aa">Protein alignments</option>
            <option value="dna">Nucleotide alignments</option>
        </param>
    </xml>

    <xml name="check_align">
        <param argument="--check-align" type="boolean" label="Check if input sequences are aligned" checked="false" truevalue="--check-align" falsevalue="" />
    </xml>

    <!-- Galaxy doesn't currently detect whether PHYLIP or NEXUS format is interleaved/sequential; if implemented update here and assoc in subcommands -->
    <xml name="collection_outputs" token_name="alignments" token_label="alignment files">
        <collection name="@NAME@_fasta" type="list" label="${tool.name} on ${on_string}: fasta">
            <discover_datasets pattern="(?P&lt;name&gt;.+-out\..+)" format="fasta" />
            <filter>out_format == "fasta"</filter>
        </collection>
        
        <collection name="@NAME@_phylip" type="list" label="${tool.name} on ${on_string}: phylip">
            <discover_datasets pattern="(?P&lt;name&gt;.+-out\..+)" format="phylip" />
            <filter>out_format == "phylip" or out_format == "phylip-int"</filter>
        </collection>
        
        <collection name="@NAME@_nexus" type="list" label="${tool.name} on ${on_string}: nexus">
            <discover_datasets pattern="(?P&lt;name&gt;.+-out\..+)" format="nex" />
            <filter>out_format == "nexus" or out_format == "nexus-int"</filter>
        </collection>
    </xml>

    <token name="@PARTITIONS_HELP@"><![CDATA[
        **What is a partitions file?**

        The partitions file maps each gene/locus to its position in the concatenated alignment. This is essential for downstream phylogenetic analyses (e.g., RAxML, IQ-TREE) that can apply different evolutionary models to different partitions.

        **Example:**

        If you concatenate three genes::

            gene1.fasta (500 bp)
            gene2.fasta (700 bp)  
            gene3.fasta (400 bp)

        The partitions file (unspecified format) will contain::

            gene1 = 1-500
            gene2 = 501-1200
            gene3 = 1201-1600

        **Partition formats:**

        - **Unspecified**
        
        ::

            gene1 = 1-500
            gene2 = 501-1200

        - **RAxML**
        
        ::

            DNA, gene1 = 1-500
            DNA, gene2 = 501-1200

        - **NEXUS**
        
        ::

            #NEXUS

            Begin sets;
                charset gene1 = 1-500;
                charset gene2 = 501-1200;
            End;
    ]]></token>

    <token name="@AMAS_SHARED_HELP@"><![CDATA[
        **Sequential vs Interleaved Phylip Format**

        - **Sequential**: Each complete sequence is written in order, one after another. Easier for programmatic parsing.

        ::

            4 60
            Seq1    ATGCATGCATATGCATGCATATGCATGCAT...
            Seq2    ATGCATGCATATGCATGCATATGCATGCAT...
            Seq3    ATGCATGCATATGCATGCATATGCATGCAT...
            Seq4    ATGCATGCATATGCATGCATATGCATGCAT...

        - **Interleaved**: Sequences are written in aligned blocks, making it easier to visually compare positions across sequences.

        ::

            4 60
            Seq1    ATGCATGCATATGCATGCAT
            Seq2    ATGCATGCATATGCATGCAT
            Seq3    ATGCATGCATATGCATGCAT
            Seq4    ATGCATGCATATGCATGCAT

            Seq1    ATGCATGCAT...
            Seq2    ATGCATGCAT...
            Seq3    ATGCATGCAT...
            Seq4    ATGCATGCAT...

        **About AMAS**

        AMAS (Alignment manipulation and summary statistics) is designed for modern phylogenomics workflows involving hundreds of taxa and thousands of loci.

        Source code and manual: https://github.com/marekborowiec/AMAS
    ]]></token>

    <xml name="citations">
        <citations>
            <citation type="doi">10.7717/peerj.1660</citation>
        </citations>
    </xml>
</macros>