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comparison gemini_load.xml @ 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 64132aa2d62a
children
comparison
equal deleted inserted replaced
8:45296e47d565 9:2270a8b83c12
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@+galaxy2"> 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@+galaxy2">
2 <description>Loading a VCF file into GEMINI</description> 2 <description>Loading a VCF file into GEMINI</description>
3 <expand macro="bio_tools"/>
3 <macros> 4 <macros>
4 <import>gemini_macros.xml</import> 5 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">load</token> 6 <token name="@BINARY@">load</token>
6 </macros> 7 </macros>
7 <expand macro="requirements" /> 8 <expand macro="requirements" />
103 <tests> 104 <tests>
104 <test> 105 <test>
105 <param name="annotation_databases" value="1999-01-01" /> 106 <param name="annotation_databases" value="1999-01-01" />
106 <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" /> 107 <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
107 <param name="opt_content" value="gene_tables,genotypes,gt_pl" /> 108 <param name="opt_content" value="gene_tables,genotypes,gt_pl" />
108 <output name="outfile" file="gemini_load_result1.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" /> 109 <output name="outfile" file="gemini_load_result1.db" ftype="gemini.sqlite" compare="sim_size" delta="10000" />
109 <assert_command> 110 <assert_command>
110 <has_text text="--skip-gerp-bp" /> 111 <has_text text="--skip-gerp-bp" />
111 <has_text text="--skip-cadd" /> 112 <has_text text="--skip-cadd" />
112 <not_has_text text="--skip-gene-tables" /> 113 <not_has_text text="--skip-gene-tables" />
113 <not_has_text text="--skip-pls" /> 114 <not_has_text text="--skip-pls" />
120 <test> 121 <test>
121 <param name="annotation_databases" value="1999-01-01" /> 122 <param name="annotation_databases" value="1999-01-01" />
122 <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" /> 123 <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
123 <param name="opt_content" value="gerp_bp,cadd,gene_tables,genotypes,gt_pl" /> 124 <param name="opt_content" value="gerp_bp,cadd,gene_tables,genotypes,gt_pl" />
124 <param name="has_genotypes" value="True" /> 125 <param name="has_genotypes" value="True" />
125 <output name="outfile" file="gemini_load_result1.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" /> 126 <output name="outfile" file="gemini_load_result1.db" ftype="gemini.sqlite" compare="sim_size" delta="10000" />
126 <assert_stderr> 127 <assert_stderr>
127 <has_text text="CADD scores are not being loaded because the annotation file could not be found." /> 128 <has_text text="CADD scores are not being loaded because the annotation file could not be found." />
128 <has_text text="GERP per bp is not being loaded because the annotation file could not be found." /> 129 <has_text text="GERP per bp is not being loaded because the annotation file could not be found." />
129 </assert_stderr> 130 </assert_stderr>
130 <assert_command> 131 <assert_command>
141 <test> 142 <test>
142 <param name="annotation_databases" value="1999-01-01" /> 143 <param name="annotation_databases" value="1999-01-01" />
143 <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" /> 144 <param name="infile" dbkey="hg19" value="gemini_load_input.vcf" ftype="vcf" />
144 <param name="opt_content" value="genotypes,gt_pl" /> 145 <param name="opt_content" value="genotypes,gt_pl" />
145 <param name="has_genotypes" value="False" /> 146 <param name="has_genotypes" value="False" />
146 <output name="outfile" file="gemini_load_result2.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" /> 147 <output name="outfile" file="gemini_load_result2.db" ftype="gemini.sqlite" compare="sim_size" delta="10000" />
147 <assert_command> 148 <assert_command>
148 <has_text text="--skip-gerp-bp" /> 149 <has_text text="--skip-gerp-bp" />
149 <has_text text="--skip-cadd" /> 150 <has_text text="--skip-cadd" />
150 <has_text text="--skip-gene-tables" /> 151 <has_text text="--skip-gene-tables" />
151 <not_has_text text="--skip-pls" /> 152 <not_has_text text="--skip-pls" />
159 <param name="annotation_databases" value="1999-01-01" /> 160 <param name="annotation_databases" value="1999-01-01" />
160 <param name="infile" dbkey="hg19" value="gemini_amend.vcf" ftype="vcf" /> 161 <param name="infile" dbkey="hg19" value="gemini_amend.vcf" ftype="vcf" />
161 <param name="opt_content" value="gene_tables,genotypes,gt_pl" /> 162 <param name="opt_content" value="gene_tables,genotypes,gt_pl" />
162 <param name="has_genotypes" value="True" /> 163 <param name="has_genotypes" value="True" />
163 <param name="ped" value="gemini_amend.ped" ftype="tabular" /> 164 <param name="ped" value="gemini_amend.ped" ftype="tabular" />
164 <output name="outfile" file="gemini_auto_rec_input.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" /> 165 <output name="outfile" file="gemini_auto_rec_input.db" ftype="gemini.sqlite" compare="sim_size" delta="20000" />
165 </test> 166 </test>
166 <test> 167 <test>
167 <param name="annotation_databases" value="1999-01-01" /> 168 <param name="annotation_databases" value="1999-01-01" />
168 <param name="infile" dbkey="hg19" value="gemini_amend.vcf.gz" ftype="vcf_bgzip" /> 169 <param name="infile" dbkey="hg19" value="gemini_amend.vcf.gz" ftype="vcf_bgzip" />
169 <param name="opt_content" value="gene_tables,genotypes,gt_pl" /> 170 <param name="opt_content" value="gene_tables,genotypes,gt_pl" />
170 <param name="has_genotypes" value="True" /> 171 <param name="has_genotypes" value="True" />
171 <param name="ped" value="gemini_amend.ped" ftype="tabular" /> 172 <param name="ped" value="gemini_amend.ped" ftype="tabular" />
172 <output name="outfile" file="gemini_auto_rec_input.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" /> 173 <output name="outfile" file="gemini_auto_rec_input.db" ftype="gemini.sqlite" compare="sim_size" delta="20000" />
173 </test> 174 </test>
174 </tests> 175 </tests>
175 <help><![CDATA[ 176 <help><![CDATA[
176 .. class:: Warning mark 177 .. class:: Warning mark
177 178