Mercurial > repos > iuc > gemini_load

comparison gemini_load.xml @ 9:aabda1846d52 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 251c6024b4ff643a63e17fbfe2590998c2bae3a7"
author iuc
date Fri, 24 Jan 2020 22:20:01 +0000
parents 7d9b78678bc2
children 269089b363d9
comparison
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8:7d9b78678bc2 9:aabda1846d52
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@+galaxy1"> 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 <macros> 3 <macros>
4 <import>gemini_macros.xml</import> 4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">load</token> 5 <token name="@BINARY@">load</token>
6 </macros> 6 </macros>
9 <expand macro="version_command" /> 9 <expand macro="version_command" />
10 <command> 10 <command>
11 <![CDATA[ 11 <![CDATA[
12 @PROVIDE_ANNO_DATA@ 12 @PROVIDE_ANNO_DATA@
13 13
14 ln -s '$infile' input.vcf && 14 ## gemini load expects a bgzipped and tabixed vcf as input
15 bgzip -c input.vcf > input.vcf.gz && 15 #set $tabixed_file = 'input.vcf.gz'
16 tabix -p vcf input.vcf.gz && 16 #if $infile.ext == 'vcf':
17 bgzip -c '$infile' > $tabixed_file &&
18 tabix -p vcf $tabixed_file &&
19 #else:
20 ln -s '$infile' $tabixed_file &&
21 ln -s '$infile.metadata.tabix_index' ${tabixed_file}.tbi &&
22 #end if
17 23
18 gemini 24 gemini
19 @BINARY@ 25 @BINARY@
20 -v input.vcf.gz 26 -v input.vcf.gz
21 #if str( $annotation_type ) != "None": 27 #if str( $annotation_type ) != "None":
54 60
55 '$outfile' 61 '$outfile'
56 ]]> 62 ]]>
57 </command> 63 </command>
58 <inputs> 64 <inputs>
59 <param name="infile" type="data" format="vcf" 65 <param name="infile" type="data" format="vcf,vcf_bgzip"
60 label="VCF dataset to be loaded in the GEMINI database" 66 label="VCF dataset to be loaded in the GEMINI database"
61 help="Only build 37 (aka hg19) of the human genome is supported."> 67 help="Only build 37 (aka hg19) of the human genome is supported.">
62 <options> 68 <options>
63 <filter type="add_value" value="hg19" /> 69 <filter type="add_value" value="hg19" />
64 <filter type="add_value" value="Homo_sapiens_nuHg19_mtrCRS" /> 70 <filter type="add_value" value="Homo_sapiens_nuHg19_mtrCRS" />
155 <param name="opt_content" value="gene_tables,genotypes,gt_pl" /> 161 <param name="opt_content" value="gene_tables,genotypes,gt_pl" />
156 <param name="has_genotypes" value="True" /> 162 <param name="has_genotypes" value="True" />
157 <param name="ped" value="gemini_amend.ped" ftype="tabular" /> 163 <param name="ped" value="gemini_amend.ped" ftype="tabular" />
158 <output name="outfile" file="gemini_auto_rec_input.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" /> 164 <output name="outfile" file="gemini_auto_rec_input.db" ftype="gemini.sqlite" compare="sim_size" delta="1000" />
159 </test> 165 </test>
166 <test>
167 <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="opt_content" value="gene_tables,genotypes,gt_pl" />
170 <param name="has_genotypes" value="True" />
171 <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 </test>
160 </tests> 174 </tests>
161 <help><![CDATA[ 175 <help><![CDATA[
162 .. class:: Warning mark 176 .. class:: Warning mark
163 177
164 **CADD scores licensing** 178 **CADD scores licensing**