Mercurial > repos > iuc > snpeff
changeset 20:8f92c2b26e6d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit fafb197acfe233d18a542e8c567943faf9abc3aa
| author | iuc |
|---|---|
| date | Fri, 25 Jan 2019 12:29:48 -0500 |
| parents | 36dc3690a82c |
| children | de67e5082c48 |
| files | snpEff.xml snpeff_get_chr_names.xml |
| diffstat | 2 files changed, 9 insertions(+), 7 deletions(-) [+] |
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--- a/snpEff.xml Wed Sep 12 14:36:04 2018 -0400 +++ b/snpEff.xml Fri Jan 25 12:29:48 2019 -0500 @@ -83,6 +83,7 @@ -configOption '${snpDb.snpeff_db.metadata.genome_version}'.codonTable='${snpDb.codon_table}' '${snpDb.snpeff_db.metadata.genome_version}' #else + -dataDir "\$PWD/temp" -download '$snpDb.genome_version' #end if @@ -170,7 +171,7 @@ </section> </when> <when value="named"> - <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)"> + <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.86)"> <help>@SNPEFF_DATABASE_URL@</help> <validator type="empty_field" message="A genome version name is required" /> </param>
--- a/snpeff_get_chr_names.xml Wed Sep 12 14:36:04 2018 -0400 +++ b/snpeff_get_chr_names.xml Fri Jan 25 12:29:48 2019 -0500 @@ -9,7 +9,7 @@ <expand macro="stdio" /> <expand macro="version_command" /> <command><![CDATA[ - snpEff dump + snpEff @JAVA_OPTIONS@ dump #if $snpDb.genomeSrc == 'cached': -dataDir ${snpDb.genomeVersion.fields.path} $snpDb.genomeVersion @@ -21,6 +21,7 @@ -configOption '${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 @@ -47,14 +48,14 @@ <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" > + <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> + <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)"> + <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> @@ -62,10 +63,10 @@ <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" > + <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> + <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>