| Previous changeset 8:45296e47d565 (2020-03-10) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd |
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modified:
gemini_load.xml gemini_macros.xml |
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added:
test-data/gemini_region_filter.tabular |
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removed:
repository_dependencies.xml |
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| diff -r 45296e47d565 -r 2270a8b83c12 gemini_load.xml --- a/gemini_load.xml Tue Mar 10 06:16:34 2020 -0400 +++ b/gemini_load.xml Wed Jul 13 15:38:57 2022 +0000 |
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| @@ -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[ |
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| diff -r 45296e47d565 -r 2270a8b83c12 gemini_macros.xml --- a/gemini_macros.xml Tue Mar 10 06:16:34 2020 -0400 +++ b/gemini_macros.xml Wed Jul 13 15:38:57 2022 +0000 |
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| @@ -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 45296e47d565 -r 2270a8b83c12 repository_dependencies.xml --- a/repository_dependencies.xml Tue Mar 10 06:16:34 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 45296e47d565 -r 2270a8b83c12 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 15:38:57 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 |