Mercurial > repos > iuc > gemini_load

changeset 9:2270a8b83c12 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
author iuc
date Wed, 13 Jul 2022 15:38:57 +0000
parents 45296e47d565
children
files gemini_load.xml gemini_macros.xml repository_dependencies.xml test-data/gemini_region_filter.tabular
diffstat 4 files changed, 52 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/gemini_load.xml	Tue Mar 10 06:16:34 2020 -0400
+++ b/gemini_load.xml	Wed Jul 13 15:38:57 2022 +0000
@@ -1,5 +1,6 @@
 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@+galaxy2">
     <description>Loading a VCF file into GEMINI</description>
+    <expand macro="bio_tools"/>
     <macros>
         <import>gemini_macros.xml</import>
         <token name="@BINARY@">load</token>
@@ -105,7 +106,7 @@
             <param name="annotation_databases" value="1999-01-01" />
             <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
             <param name="opt_content" value="gene_tables,genotypes,gt_pl" />
-            <output name="outfile" file="gemini_load_result1.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
+            <output name="outfile" file="gemini_load_result1.db" ftype="gemini.sqlite" compare="sim_size" delta="10000" />
             <assert_command>
                 <has_text text="--skip-gerp-bp" />
                 <has_text text="--skip-cadd" />
@@ -122,7 +123,7 @@
             <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
             <param name="opt_content" value="gerp_bp,cadd,gene_tables,genotypes,gt_pl" />
             <param name="has_genotypes" value="True" />
-            <output name="outfile" file="gemini_load_result1.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
+            <output name="outfile" file="gemini_load_result1.db" ftype="gemini.sqlite" compare="sim_size" delta="10000" />
             <assert_stderr>
                 <has_text text="CADD scores are not being loaded because the annotation file could not be found." />
                 <has_text text="GERP per bp is not being loaded because the annotation file could not be found." />
@@ -143,7 +144,7 @@
             <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
             <param name="opt_content" value="genotypes,gt_pl" />
             <param name="has_genotypes" value="False" />
-            <output name="outfile" file="gemini_load_result2.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
+            <output name="outfile" file="gemini_load_result2.db" ftype="gemini.sqlite" compare="sim_size" delta="10000" />
             <assert_command>
                 <has_text text="--skip-gerp-bp" />
                 <has_text text="--skip-cadd" />
@@ -161,7 +162,7 @@
             <param name="opt_content" value="gene_tables,genotypes,gt_pl" />
             <param name="has_genotypes" value="True" />
             <param name="ped" value="gemini_amend.ped" ftype="tabular" />
-            <output name="outfile" file="gemini_auto_rec_input.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
+            <output name="outfile" file="gemini_auto_rec_input.db" ftype="gemini.sqlite" compare="sim_size" delta="20000" />
         </test>
         <test>
             <param name="annotation_databases" value="1999-01-01" />
@@ -169,7 +170,7 @@
             <param name="opt_content" value="gene_tables,genotypes,gt_pl" />
             <param name="has_genotypes" value="True" />
             <param name="ped" value="gemini_amend.ped" ftype="tabular" />
-            <output name="outfile" file="gemini_auto_rec_input.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
+            <output name="outfile" file="gemini_auto_rec_input.db" ftype="gemini.sqlite" compare="sim_size" delta="20000" />
         </test>
     </tests>
     <help><![CDATA[
--- a/gemini_macros.xml	Tue Mar 10 06:16:34 2020 -0400
+++ b/gemini_macros.xml	Wed Jul 13 15:38:57 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>
--- a/repository_dependencies.xml	Tue Mar 10 06:16:34 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gemini_region_filter.tabular	Wed Jul 13 15:38:57 2022 +0000
@@ -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