| Previous changeset 7:7adfd0589f49 (2017-04-18) Next changeset 9:68693743661e (2017-11-14) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 9d2052269bfbca81a5f9cd10c3153e611358a329 |
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modified:
readme.rst snpEff.xml snpEff_macros.xml tool_data_table_conf.xml.sample |
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removed:
tool-data/snpeffv_annotations.loc.sample tool-data/snpeffv_databases.loc.sample |
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| diff -r 7adfd0589f49 -r ce135864629c readme.rst --- a/readme.rst Tue Apr 18 09:33:56 2017 -0400 +++ b/readme.rst Tue Oct 24 07:27:53 2017 -0400 |
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| @@ -13,8 +13,8 @@ There are 2 datamanagers to download and install prebuilt SnpEff genome databases: -* data_manager_snpeff_databases: generates a list of available SnpEff genome databases into the ``tool-data/snpeff_databases.loc`` file -* data_manager_snpeff_download: downloads a SnpEff genome database selected from ``tool-data/snpeff_databases.loc`` and adds entries to ``snpeff_genomedb.loc``, ``snpeff_regulationdb.loc`` and ``snpeff_annotations.loc`` +* data_manager_snpeff_databases: generates a list of available SnpEff genome databases into the ``tool-data/snpeffv_databases.loc`` file +* data_manager_snpeff_download: downloads a SnpEff genome database selected from ``tool-data/snpeffv_databases.loc`` and adds entries to ``snpeffv_genomedb.loc`` and ``snpeffv_regulationdb.loc`` . SnpEff citation: |Cingolani2012program|_. |
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| diff -r 7adfd0589f49 -r ce135864629c snpEff.xml --- a/snpEff.xml Tue Apr 18 09:33:56 2017 -0400 +++ b/snpEff.xml Tue Oct 24 07:27:53 2017 -0400 |
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| @@ -218,7 +218,7 @@ <option value="-noNextProt">Disable NextProt annotations</option> <option value="-noInteraction">Disable interaction annotations</option> <option value="-cancer">Perform 'cancer' comparisons (somatic vs. germline)</option> - <!-- onlyReg option results in ifrequent exceptions with version 4.3k + <!-- onlyReg option results in frequent exceptions with version 4.3k <option value="-onlyReg">Only use regulation tracks</option> --> </param> |
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| diff -r 7adfd0589f49 -r ce135864629c snpEff_macros.xml --- a/snpEff_macros.xml Tue Apr 18 09:33:56 2017 -0400 +++ b/snpEff_macros.xml Tue Oct 24 07:27:53 2017 -0400 |
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| @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="4.3k">snpeff</requirement> + <requirement type="package" version="4.3r">snpeff</requirement> </requirements> </xml> <xml name="stdio"> @@ -15,7 +15,7 @@ snpEff -version ]]></version_command> </xml> - <token name="@WRAPPER_VERSION@">4.3k</token> + <token name="@WRAPPER_VERSION@">4.3r</token> <token name="@SNPEFF_VERSION@">SnpEff4.3</token> <token name="@SNPEFF_DATABASE_URL@">https://sourceforge.net/projects/snpeff/files/databases/v4_3/</token> <token name="@EXTERNAL_DOCUMENTATION@"> |
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| diff -r 7adfd0589f49 -r ce135864629c tool-data/snpeffv_annotations.loc.sample --- a/tool-data/snpeffv_annotations.loc.sample Tue Apr 18 09:33:56 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,5 +0,0 @@ -## Regulation Databases for SnpEff -## These are from the list on: http://snpeff.sourceforge.net/download.html -#key snpeff_version genome annotation_name description -#SnpEff4.0_GRCh37.75 SnpEff4.0 GRCh37.75 nextprot nextprot -#SnpEff4.0_GRCh38.76 SnpEff4.1 GRCh38.76 motif motif |
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| diff -r 7adfd0589f49 -r ce135864629c tool-data/snpeffv_databases.loc.sample --- a/tool-data/snpeffv_databases.loc.sample Tue Apr 18 09:33:56 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,5 +0,0 @@ -## Available Databases for SnpEff -## These are from the list on: http://snpeff.sourceforge.net/download.html -## the Description field in this sample is "Genome : Version" -#key snpeff_version Version Description -#SnpEff4.0_GRCh37.75 SnpEff4.0 GRCh37.75 Homo sapiens : GRCh37.75 |
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| diff -r 7adfd0589f49 -r ce135864629c tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Tue Apr 18 09:33:56 2017 -0400 +++ b/tool_data_table_conf.xml.sample Tue Oct 24 07:27:53 2017 -0400 |
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| @@ -7,13 +7,4 @@ <columns>key, version, genome, value, name</columns> <file path="tool-data/snpeffv_regulationdb.loc" /> </table> - <table name="snpeffv_annotations" comment_char="#" allow_duplicate_entries="False"> - <columns>key, version, genome, value, name</columns> - <file path="tool-data/snpeffv_annotations.loc" /> - </table> - <table name="snpeffv_databases" comment_char="#" allow_duplicate_entries="False"> - <columns>key, version, value, name</columns> - <file path="tool-data/snpeffv_databases.loc" /> - </table> </tables> - |