comparison macros.xml @ 20:35d32c807c23 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets commit 5a65a62588a36d757f96681bf72f537c12c91beb

19:ced734560c9d

<macros>
    <token name="@TOOL_VERSION@">17.1.0</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">23.0</token>
    <token name="@LICENSE@">MIT</token>
    <token name="@PROFILE_AND_LICENSE@">profile="@PROFILE@" license="@LICENSE@"</token>
    <token name="@SETUP_CERTIFICATES@"><![CDATA[

[ -f /usr/local/ssl/cacert.pem ] && export SSL_CERT_FILE="/usr/local/ssl/cacert.pem";
        ]]></token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">ncbi-datasets-cli</requirement>
            <requirement type="package" version="2025.1.31">ca-certificates</requirement>
            <requirement type="package" version="6.0">unzip</requirement>
        </requirements>
    </xml>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">ncbi_datasets</xref>

        </param>
    </xml>
    <xml name="genome_includes">
        <option value="genome" selected="true">genomic sequence (genome)</option>
        <option value="rna">transcript (rna)</option>
        <option value="protein">amnio acid sequences (protein)</option>
        <option value="cds">nucleotide coding sequences (cds)</option>
        <option value="gff3">general feature file (gff3)</option>
        <option value="gtf">gene transfer format (gtf)</option>
        <option value="gbff">GenBank flat file (gbff)</option>
        <option value="seq-report">sequence report file (seq-report)</option>
        <yield/>
    </xml>
    <xml name="gene_includes">
        <option value="gene">gene sequence (gene)</option>
        <option value="protein" selected="true">amnio acid sequences (protein)</option>
        <yield/>
    </xml>

    <token name="@INCLUDE@"><![CDATA[
        --include

            </element>
        </element>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">@misc{NCBI,
                author = "{NCBI}",
                title = "NCBI Datasets",
                year = "2022",
                url = "https://github.com/ncbi/datasets"}
            </citation>
        </citations>
    </xml>
</macros>

20:35d32c807c23

<macros>
    <token name="@TOOL_VERSION@">18.13.0</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">23.0</token>
    <token name="@LICENSE@">MIT</token>
    <token name="@PROFILE_AND_LICENSE@">profile="@PROFILE@" license="@LICENSE@"</token>
    <token name="@SETUP_CERTIFICATES@"><![CDATA[

[ -f /usr/local/ssl/cacert.pem ] && export SSL_CERT_FILE="/usr/local/ssl/cacert.pem";
        ]]></token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">ncbi-datasets-cli</requirement>
            <requirement type="package" version="2025.8.3">ca-certificates</requirement>
             <!-- Removed line below because it was causing "skipping: [..] need PK compat. v4.5 (can do v2.1)"  -->
             <!-- <requirement type="package" version="6.0">unzip</requirement> -->
        </requirements>
    </xml>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">ncbi_datasets</xref>

        </param>
    </xml>
    <xml name="genome_includes">
        <option value="genome" selected="true">genomic sequence (genome)</option>
        <option value="rna">transcript (rna)</option>
        <option value="protein">amino acid sequences (protein)</option>
        <option value="cds">nucleotide coding sequences (cds)</option>
        <option value="gff3">general feature file (gff3)</option>
        <option value="gtf">gene transfer format (gtf)</option>
        <option value="gbff">GenBank flat file (gbff)</option>
        <option value="seq-report">sequence report file (seq-report)</option>
        <yield/>
    </xml>
    <xml name="gene_includes">
        <option value="gene">gene sequence (gene)</option>
        <option value="protein" selected="true">amino acid sequences (protein)</option>
        <yield/>
    </xml>

    <token name="@INCLUDE@"><![CDATA[
        --include

            </element>
        </element>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">
                10.1038/s41597-024-03571-y
            </citation>
        </citations>
    </xml>
</macros>