Repository 'gemini_amend'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/gemini_amend

Changeset 8:334e946cacd4 (2022-07-13)
Previous changeset 7:be828b79bd4d (2020-03-10)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
modified:
gemini_amend.xml
gemini_macros.xml
added:
test-data/gemini_region_filter.tabular
removed:
repository_dependencies.xml
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diff -r be828b79bd4d -r 334e946cacd4 gemini_amend.xml
--- a/gemini_amend.xml Tue Mar 10 06:19:16 2020 -0400
+++ b/gemini_amend.xml Wed Jul 13 15:29:47 2022 +0000
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@@ -1,5 +1,6 @@
 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
     <description>Amend an already loaded GEMINI database.</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>gemini_macros.xml</import>
         <token name="@BINARY@">amend</token>
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diff -r be828b79bd4d -r 334e946cacd4 gemini_macros.xml
--- a/gemini_macros.xml Tue Mar 10 06:19:16 2020 -0400
+++ b/gemini_macros.xml Wed Jul 13 15:29:47 2022 +0000
[
@@ -4,6 +4,12 @@
     <!-- minimal annotation files version required by this version of gemini -->
     <token name="@DB_VERSION@">200</token>
 
+    <xml name="bio_tools">
+        <xrefs>
+            <xref type="bio.tools">gemini</xref>
+        </xrefs>
+    </xml>
+
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">gemini</requirement>
@@ -178,7 +184,7 @@
         <repeat name="regions" title="Region Filter" default="0" min="0"
         help="Filter variant sites by their position in the genome. If multiple Region Filters are specified, all variants that fall in ONE of the regions are reported.">
             <param name="chrom" type="text" label="Chromosome">
-                <validator type="expression" message="A chromosome identifier is required when specifying a region filter">value.strip()</validator>
+                <validator type="regex" message="A chromosome identifier is required when specifying a region filter. It should start with 'chr'">^chr[0-9a-zA-Z: _.-]+</validator>
             </param>
             <param name="start" type="text" label="Region Start">
                 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
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diff -r be828b79bd4d -r 334e946cacd4 repository_dependencies.xml
--- a/repository_dependencies.xml Tue Mar 10 06:19:16 2020 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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@@ -1,4 +0,0 @@
-<?xml version="1.0" ?>
-<repositories description="This requires the GEMINI data manager definition to install all required annotation databases.">
-    <repository changeset_revision="f57426daa04d" name="data_manager_gemini_database_downloader" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/>
-</repositories>
\ No newline at end of file
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diff -r be828b79bd4d -r 334e946cacd4 test-data/gemini_region_filter.tabular
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gemini_region_filter.tabular Wed Jul 13 15:29:47 2022 +0000
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@@ -0,0 +1,39 @@
+chrom start end ref alt gene impact
+chr1 10582 10583 G A DDX11L1 upstream_gene_variant
+chr1 10610 10611 C G DDX11L1 upstream_gene_variant
+chr1 13301 13302 C T DDX11L1 exon_variant
+chr1 13326 13327 G C DDX11L1 exon_variant
+chr1 13956 13958 TC T DDX11L1 exon_variant
+chr1 13979 13980 T C DDX11L1 exon_variant
+chr1 30922 30923 G T FAM138A downstream_gene_variant
+chr1 46401 46402 C CTGT None intergenic_variant
+chr1 47189 47190 G GA None intergenic_variant
+chr1 51475 51476 T C None intergenic_variant
+chr1 51478 51479 T A None intergenic_variant
+chr1 51913 51914 T G None intergenic_variant
+chr1 51934 51935 C T None intergenic_variant
+chr1 51953 51954 G C None intergenic_variant
+chr1 52057 52058 G C None intergenic_variant
+chr1 52143 52144 T A None intergenic_variant
+chr1 52184 52188 TTAA T None intergenic_variant
+chr1 52237 52238 T G None intergenic_variant
+chr1 53233 53236 CAT C None intergenic_variant
+chr1 54352 54353 C A None intergenic_variant
+chr1 54420 54421 A G None intergenic_variant
+chr1 54489 54490 G A None intergenic_variant
+chr1 54675 54676 C T None intergenic_variant
+chr1 54752 54753 T G None intergenic_variant
+chr1 55163 55164 C A None intergenic_variant
+chr1 55248 55249 C CTATGG None intergenic_variant
+chr1 55298 55299 C T None intergenic_variant
+chr1 55312 55313 A T None intergenic_variant
+chr1 55325 55326 T C None intergenic_variant
+chr1 55329 55330 G A None intergenic_variant
+chr1 55366 55367 G A None intergenic_variant
+chr1 55387 55388 C T None intergenic_variant
+chr1 55393 55394 T A None intergenic_variant
+chr1 55415 55416 G A None intergenic_variant
+chr1 55426 55427 T C None intergenic_variant
+chr1 55815 55816 G A None intergenic_variant
+chr1 55849 55850 C G None intergenic_variant
+chr1 55851 55852 G C None intergenic_variant