Mercurial > repos > iuc > gemini_load
diff gemini_load.xml @ 4:5c5cdbdc3534 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
| author | iuc |
|---|---|
| date | Fri, 14 Dec 2018 13:01:22 -0500 |
| parents | 269c40fdcccb |
| children | b5b53c27baca |
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--- a/gemini_load.xml Wed Oct 17 13:25:58 2018 -0400 +++ b/gemini_load.xml Fri Dec 14 13:01:22 2018 -0500 @@ -1,4 +1,4 @@ -<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> +<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1"> <description>Loading a VCF file into GEMINI</description> <macros> <import>gemini_macros.xml</import> @@ -9,14 +9,13 @@ <expand macro="version_command" /> <command> <![CDATA[ + @PROVIDE_ANNO_DATA@ + ln -s "${ infile }" input.vcf && bgzip -c input.vcf > input.vcf.gz && tabix -p vcf input.vcf.gz && gemini - #if $annotation_databases: - --annotation-dir "${annotation_databases.fields.path}" - #end if @BINARY@ -v input.vcf.gz #if str( $annotation_type ) != "None": @@ -82,12 +81,45 @@ </outputs> <tests> <test> - <param name="infile" value="gemini_load_input.vcf" ftype="vcf" /> + <param name="annotation_databases" value="1999-01-01" /> + <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" /> + <param name="skip_gene_tables" value="False" /> + <param name="skip_gerp_bp" value="True" /> + <param name="skip_cadd" value="True" /> + <param name="no_genotypes" value="False" /> + <output name="outfile" file="gemini_load_result1.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_load_input.vcf" ftype="vcf" /> + <param name="skip_gene_tables" value="False" /> + <param name="skip_gerp_bp" value="False" /> + <param name="skip_cadd" value="False" /> + <param name="no_genotypes" value="False" /> + <output name="outfile" file="gemini_load_result1.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" /> + <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." /> + </assert_stderr> + </test> + <test> + <param name="annotation_databases" value="1999-01-01" /> + <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" /> <param name="skip_gene_tables" value="True" /> <param name="skip_gerp_bp" value="True" /> <param name="skip_cadd" value="True" /> <param name="no_genotypes" value="True" /> - <output name="outfile" file="gemini_load_result.db" compare="sim_size" delta="1000"/> + <output name="outfile" file="gemini_load_result2.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" ftype="vcf" /> + <param name="skip_gene_tables" value="False" /> + <param name="skip_gerp_bp" value="True" /> + <param name="skip_cadd" value="True" /> + <param name="no_genotypes" value="False" /> + <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[