| Previous changeset 6:b2c25142267e (2019-02-06) Next 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 251c6024b4ff643a63e17fbfe2590998c2bae3a7" |
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modified:
gemini_load.xml |
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added:
test-data/gemini_amend.vcf.gz |
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| diff -r b2c25142267e -r 64132aa2d62a gemini_load.xml --- a/gemini_load.xml Wed Feb 06 10:58:17 2019 -0500 +++ b/gemini_load.xml Fri Jan 24 17:33:33 2020 -0500 |
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| @@ -1,4 +1,4 @@ -<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@+galaxy1"> +<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@+galaxy2"> <description>Loading a VCF file into GEMINI</description> <macros> <import>gemini_macros.xml</import> @@ -11,9 +11,15 @@ <![CDATA[ @PROVIDE_ANNO_DATA@ - ln -s '$infile' input.vcf && - bgzip -c input.vcf > input.vcf.gz && - tabix -p vcf input.vcf.gz && + ## gemini load expects a bgzipped and tabixed vcf as input + #set $tabixed_file = 'input.vcf.gz' + #if $infile.ext == 'vcf': + bgzip -c '$infile' > $tabixed_file && + tabix -p vcf $tabixed_file && + #else: + ln -s '$infile' $tabixed_file && + ln -s '$infile.metadata.tabix_index' ${tabixed_file}.tbi && + #end if gemini @BINARY@ @@ -56,7 +62,7 @@ ]]> </command> <inputs> - <param name="infile" type="data" format="vcf" + <param name="infile" type="data" format="vcf,vcf_bgzip" label="VCF dataset to be loaded in the GEMINI database" help="Only build 37 (aka hg19) of the human genome is supported."> <options> @@ -157,6 +163,14 @@ <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" /> </test> + <test> + <param name="annotation_databases" value="1999-01-01" /> + <param name="infile" dbkey="hg19" value="gemini_amend.vcf.gz" ftype="vcf_bgzip" /> + <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" /> + </test> </tests> <help><![CDATA[ .. class:: Warning mark |
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| diff -r b2c25142267e -r 64132aa2d62a test-data/gemini_amend.vcf.gz |
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| Binary file test-data/gemini_amend.vcf.gz has changed |