Mercurial > repos > iuc > snpeff
changeset 28:6322be79bd8e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd
author | iuc |
---|---|
date | Sat, 28 Sep 2024 16:27:56 +0000 |
parents | 9473cd297a76 |
children | ca2b512e8d7c |
files | snpEff.xml snpEff_create_db.xml snpeff_get_chr_names.xml |
diffstat | 3 files changed, 22 insertions(+), 22 deletions(-) [+] |
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--- a/snpEff.xml Wed Nov 22 19:44:16 2023 +0000 +++ b/snpEff.xml Sat Sep 28 16:27:56 2024 +0000 @@ -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"> @@ -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"> @@ -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="<b>"/> + </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"/> @@ -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[
--- a/snpEff_create_db.xml Wed Nov 22 19:44:16 2023 +0000 +++ b/snpEff_create_db.xml Sat Sep 28 16:27:56 2024 +0000 @@ -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" /> @@ -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" /> @@ -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"/> @@ -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"/> @@ -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"/>
--- a/snpeff_get_chr_names.xml Wed Nov 22 19:44:16 2023 +0000 +++ b/snpeff_get_chr_names.xml Sat Sep 28 16:27:56 2024 +0000 @@ -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> @@ -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>