comparison snpeff_get_chr_names.xml @ 19:36dc3690a82c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 530737ce6054364b394db08d42e3777355fa5c05

18:dd3622f501f3

<tool id="snpEff_get_chr_names" name="SnpEff chromosome-info:" version="@wrapper_version@.galaxy1">
    <description>list chromosome names/lengths</description>
    <macros>
        <import>snpEff_macros.xml</import>
    </macros>
    <requirements>

            </param>
            <when value="cached">
                <param name="genomeVersion" type="select" label="Genome">
                    <help>This can only be used on built-in databases manually configured by your galaxy admin.</help>
                    <options from_data_table="snpeffv_genomedb">
                            <filter type="static_value" name="snpeff_version" value="@snpeff_version@" column="1"/>
                            <filter type="unique_value" column="2" />
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="snpeff_db" type="data" format="snpeffdb" label="@snpeff_version@ Genome Data">
                    <help>This can only be used on databases in your history that were downloaded using the snpEff download tool.</help>
                    <options options_filter_attribute="metadata.snpeff_version" >
                        <filter type="add_value" value="@snpeff_version@" />
                    </options>
                    <validator type="expression" message="This version of SnpEff will only work with @snpeff_version@ genome databases">value is not None and value.metadata.snpeff_version == "@snpeff_version@"</validator>
                </param>
            </when>
            <when value="named">
                <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
                    <help>The list of available databases can be obtained with 'SnpEff databases' tool. If the database name is not found, locate a database here and download it in your history.</help>
                    <validator type="regex" message="A genome version name is required">\S+</validator>
                </param>
            </when>
            <when value="custom">
                <param name="snpeff_db" type="data" format="snpeffdb" label="@snpeff_version@ Genome Data">
                    <help>This can only be used on databases in your history that were created using the snpEff build tool.</help>
                    <options options_filter_attribute="metadata.snpeff_version" >
                        <filter type="add_value" value="@snpeff_version@" />
                    </options>
                    <validator type="expression" message="This version of SnpEff will only work with @snpeff_version@ genome databases">value is not None and value.metadata.snpeff_version == "@snpeff_version@"</validator>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>

19:36dc3690a82c

<tool id="snpEff_get_chr_names" name="SnpEff chromosome-info:" version="@WRAPPER_VERSION@.galaxy1">
    <description>list chromosome names/lengths</description>
    <macros>
        <import>snpEff_macros.xml</import>
    </macros>
    <requirements>

            </param>
            <when value="cached">
                <param name="genomeVersion" type="select" label="Genome">
                    <help>This can only be used on built-in databases manually configured by your galaxy admin.</help>
                    <options from_data_table="snpeffv_genomedb">
                            <filter type="static_value" name="SNPEFF_VERSION" value="@SNPEFF_VERSION@" column="1"/>
                            <filter type="unique_value" column="2" />
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
                    <help>This can only be used on databases in your history that were downloaded using the snpEff download tool.</help>
                    <options options_filter_attribute="metadata.SNPEFF_VERSION" >
                        <filter type="add_value" value="@SNPEFF_VERSION@" />
                    </options>
                    <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.SNPEFF_VERSION == "@SNPEFF_VERSION@"</validator>
                </param>
            </when>
            <when value="named">
                <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
                    <help>The list of available databases can be obtained with 'SnpEff databases' tool. If the database name is not found, locate a database here and download it in your history.</help>
                    <validator type="regex" message="A genome version name is required">\S+</validator>
                </param>
            </when>
            <when value="custom">
                <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
                    <help>This can only be used on databases in your history that were created using the snpEff build tool.</help>
                    <options options_filter_attribute="metadata.SNPEFF_VERSION" >
                        <filter type="add_value" value="@SNPEFF_VERSION@" />
                    </options>
                    <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.SNPEFF_VERSION == "@SNPEFF_VERSION@"</validator>
                </param>
            </when>
        </conditional>
    </inputs>
    <outputs>