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Merge pull request #6356 from bernt-matthias/lint-snpeff
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linter fixes for snpeff
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@bgruening
bgruening authored Sep 28, 2024
2 parents 82eef3f + 6ad64a1 commit 4bc3ef8
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Showing 4 changed files with 22 additions and 25 deletions.
3 changes: 0 additions & 3 deletions tool_collections/snpeff/.lint_skip
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28 changes: 17 additions & 11 deletions tool_collections/snpeff/snpEff.xml
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Expand Up @@ -159,9 +159,6 @@
</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">
Expand All @@ -181,9 +178,6 @@
</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">
Expand Down Expand Up @@ -364,30 +358,35 @@
</change_format>
</data>
<data name="statsFile" format="html" label="${tool.name} on ${on_string} - HTML stats">
<filter>generate_stats == True</filter>
<filter>generate_stats</filter>
</data>
<data name="csvFile" format="csv" label="${tool.name} on ${on_string} - CSV stats">
<filter>csvStats == True</filter>
<filter>csvStats</filter>
</data>
</outputs>
<tests>
<test>
<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="false"/>
<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>
<test expect_num_outputs="2">
<param name="input" ftype="vcf" value="input.vcf"/>
<param name="inputFormat" value="vcf"/>
<param name="outputFormat" value="vcf"/>
Expand All @@ -396,12 +395,19 @@
<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[
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10 changes: 5 additions & 5 deletions tool_collections/snpeff/snpEff_create_db.xml
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Expand Up @@ -124,7 +124,7 @@
</data>
</outputs>
<tests>
<test>
<test expect_num_outputs="2">
<param name="genome_version" value="pBR322"/>
<param name="input_type_selector" value="gb"/>
<param name="input" value="pBR322.gbk" />
Expand All @@ -135,7 +135,7 @@
</output>
<output name="output_fasta" value="pBR322_test1.fna"/>
</test>
<test>
<test expect_num_outputs="2">
<param name="genome_version" value="pBR322"/>
<param name="input_type_selector" value="gb"/>
<param name="input" value="pBR322.gbk.gz" />
Expand All @@ -146,7 +146,7 @@
</output>
<output name="output_fasta" value="pBR322_test1.fna"/>
</test>
<test>
<test expect_num_outputs="1">
<param name="genome_version" value="pBR322"/>
<param name="input_type_selector" value="gff"/>
<param name="reference_source_selector" value="history"/>
Expand All @@ -158,7 +158,7 @@
</assert_contents>
</output>
</test>
<test>
<test expect_num_outputs="1">
<param name="genome_version" value="pBR322"/>
<param name="input_type_selector" value="gff"/>
<param name="reference_source_selector" value="history"/>
Expand All @@ -170,7 +170,7 @@
</assert_contents>
</output>
</test>
<test>
<test expect_num_outputs="1">
<param name="genome_version" value="Saccharomyces_mito"/>
<param name="input_type_selector" value="gtf"/>
<param name="reference_source_selector" value="history"/>
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6 changes: 0 additions & 6 deletions tool_collections/snpeff/snpeff_get_chr_names.xml
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Expand Up @@ -50,9 +50,6 @@
<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>
Expand All @@ -65,9 +62,6 @@
<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>
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