| Previous changeset 1:c3da7c5f2141 (2016-03-22) Next changeset 3:40f85b45e472 (2018-10-17) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0 |
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modified:
gemini_dump.xml gemini_macros.xml repository_dependencies.xml tool_data_table_conf.xml.sample |
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| diff -r c3da7c5f2141 -r a32c298053e4 gemini_dump.xml --- a/gemini_dump.xml Tue Mar 22 21:43:09 2016 -0400 +++ b/gemini_dump.xml Thu Nov 09 13:18:08 2017 -0500 |
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| @@ -26,8 +26,8 @@ <option value="--genotypes">All rows/columns from the variants table with one line per sample/genotype (--genotypes)</option> <option value="--samples">All rows/columns from the samples table (--samples)</option> </param> - <param argument="--header" type="boolean" label="Include a header of column names" truevalue="--header" falsevalue="" selected="False" /> - <param argument="--tfam" type="boolean" label="Output sample information to TFAM information" truevalue="--tfam" falsevalue="" selected="False" /> + <param argument="--header" type="boolean" label="Include a header of column names" truevalue="--header" falsevalue="" checked="False" /> + <param argument="--tfam" type="boolean" label="Output sample information to TFAM information" truevalue="--tfam" falsevalue="" checked="False" /> </inputs> <outputs> <data name="outfile" format="tabular" /> |
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| diff -r c3da7c5f2141 -r a32c298053e4 gemini_macros.xml --- a/gemini_macros.xml Tue Mar 22 21:43:09 2016 -0400 +++ b/gemini_macros.xml Thu Nov 09 13:18:08 2017 -0500 |
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| @@ -3,6 +3,8 @@ <requirements> <requirement type="package" version="0.18.1">gemini</requirement> <requirement type="package" version="0.2.6">tabix</requirement> + <!-- for conda useage --> + <!--requirement type="package" version="1.3.1">htslib</requirement--> <yield /> </requirements> </xml> @@ -63,6 +65,7 @@ <option value="impact_severity">impact_severity</option> <option value="max_aaf_all">alternative allele frequency</option> </param> + <param name="extra_cols" type="text" label="Additional columns." help="Separate by whitespace"/> </when> </conditional> </xml> @@ -96,6 +99,16 @@ #end if </token> + <token name="@COLUMN_SELECT@"> + #if $report.report_selector != 'all': + --columns "${report.columns} + #if str($report.extra_cols).strip() + #echo ','+','.join(str($report.extra_cols).split()) + #end if + " + #end if + </token> + <xml name="family"> <param name="families" type="text" value="" label="Comma seperated list of families to restrict the analysis to." help="e.g. Family1,Family3 (--families)"/> </xml> |
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| diff -r c3da7c5f2141 -r a32c298053e4 repository_dependencies.xml --- a/repository_dependencies.xml Tue Mar 22 21:43:09 2016 -0400 +++ b/repository_dependencies.xml Thu Nov 09 13:18:08 2017 -0500 |
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| @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="This requires the GEMINI data manager definition to install all required annotation databases."> - <repository changeset_revision="345412d58d75" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="172815da3d41" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </repositories> |
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| diff -r c3da7c5f2141 -r a32c298053e4 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Tue Mar 22 21:43:09 2016 -0400 +++ b/tool_data_table_conf.xml.sample Thu Nov 09 13:18:08 2017 -0500 |
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| @@ -1,5 +1,5 @@ <tables> - <table name="gemini_databases" comment_char="#"> + <table name="gemini_databases" comment_char="#" allow_duplicate_entries="False"> <columns>value, dbkey, name, path</columns> <file path="tool-data/gemini_databases.loc" /> </table> |