Mercurial > repos > jjohnson > snpeff
changeset 21:c780e3f75b3d
Filter genome history snpeffdb by snpeff_version
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 14 Jan 2015 12:03:21 -0600 |
| parents | 7a46f9a72d3c |
| children | bb0797deab78 |
| files | repository_dependencies.xml snpEff.xml snpEff_download.xml snpEff_macros.xml |
| diffstat | 4 files changed, 12 insertions(+), 7 deletions(-) [+] |
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--- a/repository_dependencies.xml Tue Jan 13 16:01:31 2015 -0600 +++ b/repository_dependencies.xml Wed Jan 14 12:03:21 2015 -0600 @@ -1,5 +1,4 @@ <?xml version="1.0"?> <repositories description="This requires the SnpEff datatype definitions."> - <repository name="snpeff_datatypes" owner="jjohnson" changeset_revision="9efd0d32fe8a" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> - <repository name="snpeff_datatype_v4_0" owner="jjohnson" changeset_revision="dc8dfd3f9da8" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + <repository name="snpeff_datatypes" owner="jjohnson" changeset_revision="5d6f3622b99d" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> </repositories>
--- a/snpEff.xml Tue Jan 13 16:01:31 2015 -0600 +++ b/snpEff.xml Wed Jan 14 12:03:21 2015 -0600 @@ -1,4 +1,4 @@ -<tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.2"> +<tool id="snpEff" name="SnpEff" version="@WRAPPER_VERSION@.3"> <description>Variant effect and annotation</description> <expand macro="requirements" /> <macros> @@ -118,7 +118,7 @@ <param name="genomeVersion" type="select" label="Genome"> <!--GENOME DESCRIPTION--> <options from_data_table="snpeffv_genomedb"> - <filter type="static_value" name="snpeff_version" value="SnpEff4.0" column="1"/> + <filter type="static_value" name="snpeff_version" value="@SNPEFF_VERSION@" column="1"/> <filter type="unique_value" column="2" /> </options> </param> @@ -138,7 +138,12 @@ </param> </when> <when value="history"> - <param format="snpeffdbv40" name="snpeff_db" type="data" label="SnpEff Genome Version Data"/> + <param format="snpeffdb" name="snpeff_db" type="data" 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> <!-- From metadata --> <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional annotations"> <help>These are available for only a few genomes</help>
--- a/snpEff_download.xml Tue Jan 13 16:01:31 2015 -0600 +++ b/snpEff_download.xml Wed Jan 14 12:03:21 2015 -0600 @@ -1,4 +1,4 @@ -<tool id="snpEff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.2"> +<tool id="snpEff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.3"> <description>Download a new database</description> <expand macro="requirements" /> <macros> @@ -16,7 +16,7 @@ </param> </inputs> <outputs> - <data format="snpeffdbv40" name="snpeff_db" label="${tool.name} ${genome_version}" /> + <data format="snpeffdb" name="snpeff_db" label="${tool.name} @SNPEFF_VERSION@ ${genome_version}" /> </outputs> <expand macro="stdio" /> <help>
--- a/snpEff_macros.xml Tue Jan 13 16:01:31 2015 -0600 +++ b/snpEff_macros.xml Wed Jan 14 12:03:21 2015 -0600 @@ -11,6 +11,7 @@ </stdio> </xml> <token name="@WRAPPER_VERSION@">4.0</token> + <token name="@SNPEFF_VERSION@">SnpEff4.0</token> <token name="@SNPEFF_DATABASE_URL@">http://sourceforge.net/projects/snpeff/files/databases/v4_0/</token> <token name="@EXTERNAL_DOCUMENTATION@">