comparison snpeff_get_chr_names.xml @ 20:8f92c2b26e6d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit fafb197acfe233d18a542e8c567943faf9abc3aa

19:36dc3690a82c

        <expand macro="requirement" />
    </requirements>
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
      snpEff dump
      #if $snpDb.genomeSrc == 'cached':
        -dataDir ${snpDb.genomeVersion.fields.path}
        $snpDb.genomeVersion
      #elif $snpDb.genomeSrc == 'history':
        -dataDir '${snpDb.snpeff_db.extra_files_path}'

      #elif $snpDb.genomeSrc == 'custom':
          -dataDir '${snpDb.snpeff_db.extra_files_path}'
          -configOption '${snpDb.snpeff_db.metadata.genome_version}'.genome='${snpDb.snpeff_db.metadata.genome_version}'
          '${snpDb.snpeff_db.metadata.genome_version}'
      #else
        -download
        '$snpDb.genome_version'
      #end if
      | awk '/# Chromosomes/{y=1;next}y' | grep "#" | grep -E "[0-9]" | awk 'BEGIN {err=1;} {c=$0;sub(/^[^a-zA-Z0-9_]+/, "", c) && err=0; sub(/[^a-zA-Z0-9_]+/, "\t", c) && err=0; sub(/[^0-9]*$/, "", c) && err=0; print c } END {exit err}' > '$chr_names'
    ]]></command>

                </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>

20:8f92c2b26e6d

        <expand macro="requirement" />
    </requirements>
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
      snpEff @JAVA_OPTIONS@ dump
      #if $snpDb.genomeSrc == 'cached':
        -dataDir ${snpDb.genomeVersion.fields.path}
        $snpDb.genomeVersion
      #elif $snpDb.genomeSrc == 'history':
        -dataDir '${snpDb.snpeff_db.extra_files_path}'

      #elif $snpDb.genomeSrc == 'custom':
          -dataDir '${snpDb.snpeff_db.extra_files_path}'
          -configOption '${snpDb.snpeff_db.metadata.genome_version}'.genome='${snpDb.snpeff_db.metadata.genome_version}'
          '${snpDb.snpeff_db.metadata.genome_version}'
      #else
        -dataDir "\$PWD/temp"
        -download
        '$snpDb.genome_version'
      #end if
      | awk '/# Chromosomes/{y=1;next}y' | grep "#" | grep -E "[0-9]" | awk 'BEGIN {err=1;} {c=$0;sub(/^[^a-zA-Z0-9_]+/, "", c) && err=0; sub(/[^a-zA-Z0-9_]+/, "\t", c) && err=0; sub(/[^0-9]*$/, "", c) && err=0; print c } END {exit err}' > '$chr_names'
    ]]></command>

                </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. GRCh38.86)">
                    <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>