Mercurial > repos > iuc > gemini_load

comparison gemini_load.xml @ 5:b382ddaf8445 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
author iuc
date Fri, 14 Dec 2018 12:36:51 -0500
parents 264f4601dd1d
children 424f44e3448d
comparison
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4:264f4601dd1d 5:b382ddaf8445
79 <outputs> 79 <outputs>
80 <data name="outfile" format="gemini.sqlite" /> 80 <data name="outfile" format="gemini.sqlite" />
81 </outputs> 81 </outputs>
82 <tests> 82 <tests>
83 <test> 83 <test>
84 <param name="infile" value="gemini_load_input.vcf" ftype="vcf" /> 84 <param name="annotation_databases" value="1999-01-01" />
85 <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
86 <param name="skip_gene_tables" value="False" />
87 <param name="skip_gerp_bp" value="True" />
88 <param name="skip_cadd" value="True" />
89 <param name="no_genotypes" value="False" />
90 <output name="outfile" file="gemini_load_result1.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
91 </test>
92 <test>
93 <param name="annotation_databases" value="1999-01-01" />
94 <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
95 <param name="skip_gene_tables" value="False" />
96 <param name="skip_gerp_bp" value="False" />
97 <param name="skip_cadd" value="False" />
98 <param name="no_genotypes" value="False" />
99 <output name="outfile" file="gemini_load_result1.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
100 <assert_stderr>
101 <has_text text="CADD scores are not being loaded because the annotation file could not be found." />
102 <has_text text="GERP per bp is not being loaded because the annotation file could not be found." />
103 </assert_stderr>
104 </test>
105 <test>
106 <param name="annotation_databases" value="1999-01-01" />
107 <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
85 <param name="skip_gene_tables" value="True" /> 108 <param name="skip_gene_tables" value="True" />
86 <param name="skip_gerp_bp" value="True" /> 109 <param name="skip_gerp_bp" value="True" />
87 <param name="skip_cadd" value="True" /> 110 <param name="skip_cadd" value="True" />
88 <param name="no_genotypes" value="True" /> 111 <param name="no_genotypes" value="True" />
89 <output name="outfile" file="gemini_load_result.db" compare="sim_size" delta="1000"/> 112 <output name="outfile" file="gemini_load_result2.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
113 </test>
114 <test>
115 <param name="annotation_databases" value="1999-01-01" />
116 <param name="infile" dbkey="hg19" value="gemini_amend.vcf" ftype="vcf" />
117 <param name="skip_gene_tables" value="False" />
118 <param name="skip_gerp_bp" value="True" />
119 <param name="skip_cadd" value="True" />
120 <param name="no_genotypes" value="False" />
121 <param name="ped" value="gemini_amend.ped" ftype="tabular" />
122 <output name="outfile" file="gemini_auto_rec_input.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
90 </test> 123 </test>
91 </tests> 124 </tests>
92 <help><![CDATA[ 125 <help><![CDATA[
93 **What it does** 126 **What it does**
94 127