Mercurial > repos > iuc > snpeff
changeset 30:0c8a8cd9dd5b 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 16:27:42 +0000 |
| parents | 030fe29d4c47 |
| children | b7029a54f73e |
| files | snpEff.xml snpEff_create_db.xml snpeff_get_chr_names.xml test-data/intervals.bed |
| diffstat | 4 files changed, 56 insertions(+), 32 deletions(-) [+] |
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--- a/snpEff.xml Wed Aug 03 16:33:10 2022 +0000 +++ b/snpEff.xml Sat Sep 28 16:27:42 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="snpEff" name="SnpEff eff:" version="@WRAPPER_VERSION@.galaxy1"> +<tool id="snpEff" name="SnpEff eff:" version="@WRAPPER_VERSION@.galaxy2"> <description> annotate variants</description> <macros> <import>snpEff_macros.xml</import> @@ -9,6 +9,9 @@ <expand macro="stdio" /> <expand macro="version_command" /> <command><![CDATA[ + #if $intervals + ln -s '${intervals}' intervals.bed && + #end if snpEff @JAVA_OPTIONS@ eff -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength #if $spliceSiteSize and str($spliceSiteSize) != '': @@ -42,7 +45,7 @@ -onlyTr '$transcripts' #end if #if $intervals ### fix this for multiple dataset input - -interval '$intervals' + -interval intervals.bed #end if #if $statsFile: -stats '$statsFile' @@ -156,9 +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"> @@ -178,9 +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"> @@ -361,27 +358,56 @@ </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 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[
--- a/snpEff_create_db.xml Wed Aug 03 16:33:10 2022 +0000 +++ b/snpEff_create_db.xml Sat Sep 28 16:27:42 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="snpEff_build_gb" name="SnpEff build:" version="@WRAPPER_VERSION@.galaxy5"> +<tool id="snpEff_build_gb" name="SnpEff build:" version="@WRAPPER_VERSION@.galaxy6" profile="22.01"> <description> database from Genbank or GFF record</description> <macros> <import>snpEff_macros.xml</import> @@ -14,25 +14,26 @@ python3 '$__tool_directory__/gbk2fa.py' '${input_type.input}' '${output_fasta}' ${input_type.remove_version} && #end if - mkdir -p '${snpeff_output.files_path}'/'${genome_version}' && + mkdir -p '${snpeff_output.files_path}/${genome_version}' && + mkdir -p snpeff_output/'${genome_version}' && #if str($input_type.input_type_selector) == "gb": #if $input_type.input.is_of_type("genbank"): - ln -s '${input_type.input}' '${snpeff_output.files_path}/${genome_version}/genes.gbk' && + ln -s '${input_type.input}' 'snpeff_output/${genome_version}/genes.gbk' && #elif $input_type.input.is_of_type("genbank.gz"): - ln -s '${input_type.input}' '${snpeff_output.files_path}/${genome_version}/genes.gbk.gz' && + ln -s '${input_type.input}' 'snpeff_output/${genome_version}/genes.gbk.gz' && #end if #else: #if $input_type.reference_source.reference_source_selector == "history": #if $input_type.reference_source.input_fasta.is_of_type("fasta"): - ln -s '${input_type.reference_source.input_fasta}' '${snpeff_output.files_path}/${genome_version}/sequences.fa' && + ln -s '${input_type.reference_source.input_fasta}' 'snpeff_output/${genome_version}/sequences.fa' && #elif $input_type.reference_source.input_fasta.is_of_type("fasta.gz"): - ln -s '${input_type.reference_source.input_fasta}' '${snpeff_output.files_path}/${genome_version}/sequences.fa.gz' && + ln -s '${input_type.reference_source.input_fasta}' 'snpeff_output/${genome_version}/sequences.fa.gz' && #end if #elif $input_type.reference_source.reference_source_selector == "cached": - ln -s '${input_type.reference_source.ref_file.fields.path}' '${snpeff_output.files_path}/${genome_version}/sequences.fa' && + ln -s '${input_type.reference_source.ref_file.fields.path}' 'snpeff_output/${genome_version}/sequences.fa' && #end if - ln -s '${input_type.input}' '${snpeff_output.files_path}/${genome_version}/genes.${input_type.input_type_selector}' && + ln -s '${input_type.input}' 'snpeff_output/${genome_version}/genes.${input_type.input_type_selector}' && #end if snpEff @JAVA_OPTIONS@ build -v @@ -45,7 +46,8 @@ #elif str($input_type.input_type_selector) == "gtf": -gtf22 #end if - -dataDir '${snpeff_output.files_path}' '${genome_version}' && + -dataDir "\$(pwd)/snpeff_output" '${genome_version}' && + mv snpeff_output/'${genome_version}'/*.bin '${snpeff_output.files_path}/${genome_version}' && echo '${genome_version}.genome : ${genome_version}' >> '${snpeff_output.files_path}'/snpEff.config && echo '${genome_version}.codonTable : ${codon_table}' >> '${snpeff_output.files_path}'/snpEff.config ]]></command> @@ -122,7 +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" /> @@ -133,7 +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" /> @@ -144,7 +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"/> @@ -156,7 +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"/> @@ -168,7 +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 Aug 03 16:33:10 2022 +0000 +++ b/snpeff_get_chr_names.xml Sat Sep 28 16:27:42 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>