| Previous changeset 1:3859552a63d8 (2016-03-22) Next changeset 3:8f53b238a360 (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_annotate.xml gemini_macros.xml repository_dependencies.xml tool_data_table_conf.xml.sample |
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| diff -r 3859552a63d8 -r 8da05bf2b1d1 gemini_annotate.xml --- a/gemini_annotate.xml Tue Mar 22 21:42:26 2016 -0400 +++ b/gemini_annotate.xml Thu Nov 09 13:18:45 2017 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> +<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1"> <description>adding your own custom annotations</description> <macros> <import>gemini_macros.xml</import> @@ -10,11 +10,13 @@ <command> <![CDATA[ - bgzip -c "$annotate_source" > tabixed.gz && - tabix -p bed tabixed.gz && + ## For GEMINI to work correctly, tabixed file must have form [name].[bed|vcf].gz + #set $tabixed_file = "tabixed.%s.gz" % $annotate_source.ext + bgzip -c "$annotate_source" > $tabixed_file && + tabix -p "$annotate_source.ext" $tabixed_file && gemini @BINARY@ - -f tabixed.gz + -f $tabixed_file -c $column_name -a $a.a_selector #if $a.a_selector == 'extract': @@ -30,7 +32,7 @@ </command> <inputs> <expand macro="infile" /> - <param name="annotate_source" type="data" format="bed" label="File containing the annotations in BED format" help="(-f)"/> + <param name="annotate_source" type="data" format="vcf,bed" label="File containing the annotations in BED/VCF format" help="(-f)"/> <param name="column_name" type="text" value="" label="The name of the column to be added to the variant table" @@ -45,12 +47,12 @@ <param name="a_selector" type="select" label="How should the annotation file be used?" help="(-a)"> <option value="boolean">Did a variant overlap a region or not? (boolean)</option> <option value="count">How many regions did a variant overlap? (count)</option> - <option value="extract" selected="True">Extract specific values from a BED file. (extract)</option> + <option value="extract" selected="True">Extract specific values from a BED/VCF file. (extract)</option> </param> <when value="extract"> - <param name="column_extracts" label="Column to extract information from for list annotations" - type="data_column" data_ref="annotate_source" force_select="true" help="(-e)"/> + <param name="column_extracts" label="Column to extract information from for list annotations. For BED files, this is the column number. For VCF files, this is the name of the INFO field." + type="text" force_select="true" help="(-e)"/> <param name="column_type" type="select" label="What data type(s) should be used to represent the new values in the database?" |
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| diff -r 3859552a63d8 -r 8da05bf2b1d1 gemini_macros.xml --- a/gemini_macros.xml Tue Mar 22 21:42:26 2016 -0400 +++ b/gemini_macros.xml Thu Nov 09 13:18:45 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 3859552a63d8 -r 8da05bf2b1d1 repository_dependencies.xml --- a/repository_dependencies.xml Tue Mar 22 21:42:26 2016 -0400 +++ b/repository_dependencies.xml Thu Nov 09 13:18:45 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 3859552a63d8 -r 8da05bf2b1d1 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Tue Mar 22 21:42:26 2016 -0400 +++ b/tool_data_table_conf.xml.sample Thu Nov 09 13:18:45 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> |