comparison snpEff.xml @ 28:6322be79bd8e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd

27:9473cd297a76

                    </param>
                </section>
            </when>
            <when value="history">
                <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
                    <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>
                <section name="reg_section" expanded="false" title="Regulation options">
                    <!-- From metadata -->
                    <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation" help="These are available for only a few genomes">

                    <validator type="empty_field" message="A genome version name is required" />
                </param>
            </when>
            <when value="custom">
                <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
                    <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>
                <param name="codon_table" type="select" label="Select genetic code for this sequence" help="If this sequence uses non-standard genetic code, select one from these options">
                    <option selected="true" value="Standard">Standard</option>
                    <option value="Vertebrate_Mitochondrial">Vertebrate_Mitochondrial</option>

                <when input="outputConditional.outputFormat" value="bed" format="bed" />
                <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
            </change_format>
        </data>
        <data name="statsFile" format="html" label="${tool.name} on ${on_string} - HTML stats">
            <filter>generate_stats == True</filter>
        </data>
        <data name="csvFile" format="csv" label="${tool.name} on ${on_string} - CSV stats">
            <filter>csvStats == True</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" ftype="vcf" value="input.vcf"/>
            <param name="inputFormat" value="vcf"/>
            <param name="outputFormat" value="vcf"/>
            <param name="genomeSrc" value="named"/>
            <param name="genome_version" value="ebola_zaire"/>
            <param name="udLength" value="0"/>
            <param name="generate_stats" value="false"/>
            <output name="snpeff_output">
                <assert_contents>
                    <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
                    <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
                </assert_contents>
            </output>
        </test>
        <!-- Test interval option-->
        <test>
            <param name="input" ftype="vcf" value="input.vcf"/>
            <param name="inputFormat" value="vcf"/>
            <param name="outputFormat" value="vcf"/>
            <param name="genomeSrc" value="named"/>
            <param name="interval" value="intervals.bed"/>
            <param name="genome_version" value="ebola_zaire"/>
            <param name="udLength" value="0"/>
            <param name="generate_stats" value="false"/>
            <output name="snpeff_output">
                <assert_contents>
                    <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
                    <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

28:6322be79bd8e

                    </param>
                </section>
            </when>
            <when value="history">
                <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
                    <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>
                <section name="reg_section" expanded="false" title="Regulation options">
                    <!-- From metadata -->
                    <param name="regulation" type="select" display="checkboxes" multiple="true" label="Non-coding and regulatory annotation" help="These are available for only a few genomes">

                    <validator type="empty_field" message="A genome version name is required" />
                </param>
            </when>
            <when value="custom">
                <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
                    <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>
                <param name="codon_table" type="select" label="Select genetic code for this sequence" help="If this sequence uses non-standard genetic code, select one from these options">
                    <option selected="true" value="Standard">Standard</option>
                    <option value="Vertebrate_Mitochondrial">Vertebrate_Mitochondrial</option>

                <when input="outputConditional.outputFormat" value="bed" format="bed" />
                <when input="outputConditional.outputFormat" value="bedAnn" format="bed" />
            </change_format>
        </data>
        <data name="statsFile" format="html" label="${tool.name} on ${on_string} - HTML stats">
            <filter>generate_stats</filter>
        </data>
        <data name="csvFile" format="csv" label="${tool.name} on ${on_string} - CSV stats">
            <filter>csvStats</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <param name="input" ftype="vcf" value="input.vcf"/>
            <param name="inputFormat" value="vcf"/>
            <param name="outputFormat" value="vcf"/>
            <param name="genomeSrc" value="named"/>
            <param name="genome_version" value="ebola_zaire"/>
            <param name="udLength" value="0"/>
            <param name="generate_stats" value="true"/>
            <output name="snpeff_output">
                <assert_contents>
                    <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
                    <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
                </assert_contents>
            </output>
            <output name="statsFile">
                <assert_contents>
                    <has_text text="&lt;b&gt;"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test interval option-->
        <test expect_num_outputs="2">
            <param name="input" ftype="vcf" value="input.vcf"/>
            <param name="inputFormat" value="vcf"/>
            <param name="outputFormat" value="vcf"/>
            <param name="genomeSrc" value="named"/>
            <param name="interval" value="intervals.bed"/>
            <param name="genome_version" value="ebola_zaire"/>
            <param name="udLength" value="0"/>
            <param name="generate_stats" value="false"/>
            <param name="csvStats" value="true"/>
            <output name="snpeff_output">
                <assert_contents>
                    <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
                    <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
                </assert_contents>
            </output>
            <output name="csvFile">
                <assert_contents>
                    <has_n_lines n="185"/>
                    <has_n_columns n="1" sep=","/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**