Mercurial > repos > iuc > gemini_mendel_errors
diff gemini_macros.xml @ 4:00c2734b3bea draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
author | iuc |
---|---|
date | Fri, 14 Dec 2018 12:45:48 -0500 |
parents | 61343646155c |
children |
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--- a/gemini_macros.xml Wed Oct 17 13:31:29 2018 -0400 +++ b/gemini_macros.xml Fri Dec 14 12:45:48 2018 -0500 @@ -1,7 +1,12 @@ <macros> + <!-- gemini version to be used --> + <token name="@VERSION@">0.18.1</token> + <!-- minimal annotation files version required by this version of gemini --> + <token name="@DB_VERSION@">181</token> + <xml name="requirements"> <requirements> - <requirement type="package" version="0.18.1">gemini</requirement> + <requirement type="package" version="@VERSION@">gemini</requirement> <requirement type="package" version="0.2.6">tabix</requirement> <!-- for conda useage --> <!--requirement type="package" version="1.3.1">htslib</requirement--> @@ -23,9 +28,10 @@ </xml> <xml name="annotation_dir"> - <param name="annotation_databases" type="select" optional="True" label="Choose a gemini annotation database"> - <options from_data_table="gemini_databases"> + <param name="annotation_databases" type="select" label="Choose a gemini annotation source"> + <options from_data_table="gemini_versioned_databases"> <filter type="sort_by" column="0" /> + <filter type="static_value" column="2" value="@DB_VERSION@" /> </options> </param> </xml> @@ -97,6 +103,12 @@ </sanitizer> </xml> + <token name="@PROVIDE_ANNO_DATA@"><![CDATA[ + mkdir gemini && + ln -s "${annotation_databases.fields.path}/gemini/data" gemini/data && + export GEMINI_CONFIG="${annotation_databases.fields.path}" && + ]]></token> + <token name="@MULTILN_SQL_EXPR_TO_CMDLN@"> #set $sql_expr = str($multiline_sql_expr).strip() #if str($sql_expr): @@ -153,7 +165,6 @@ <xml name="gt_pl_max"> <param name="gt_pl_max" type="integer" value="-1" min="-1" label="The maximum phred-scaled genotype likelihod (PL) allowed for each sample in a family" help="default: -1 (not set) (--gt-pl-max)" /> </xml> - <token name="@VERSION@">0.18.1</token> <xml name="citations"> <citations>