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comparison gemini_load.xml @ 4:5c5cdbdc3534 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 13:01:22 -0500
parents 269c40fdcccb
children b5b53c27baca
comparison
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3:cf61daf064fe 4:5c5cdbdc3534
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
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>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <expand macro="stdio" /> 8 <expand macro="stdio" />
9 <expand macro="version_command" /> 9 <expand macro="version_command" />
10 <command> 10 <command>
11 <![CDATA[ 11 <![CDATA[
12 @PROVIDE_ANNO_DATA@
13
12 ln -s "${ infile }" input.vcf && 14 ln -s "${ infile }" input.vcf &&
13 bgzip -c input.vcf > input.vcf.gz && 15 bgzip -c input.vcf > input.vcf.gz &&
14 tabix -p vcf input.vcf.gz && 16 tabix -p vcf input.vcf.gz &&
15 17
16 gemini 18 gemini
17 #if $annotation_databases:
18 --annotation-dir "${annotation_databases.fields.path}"
19 #end if
20 @BINARY@ 19 @BINARY@
21 -v input.vcf.gz 20 -v input.vcf.gz
22 #if str( $annotation_type ) != "None": 21 #if str( $annotation_type ) != "None":
23 -t "$annotation_type" 22 -t "$annotation_type"
24 #end if 23 #end if
80 <outputs> 79 <outputs>
81 <data name="outfile" format="gemini.sqlite" /> 80 <data name="outfile" format="gemini.sqlite" />
82 </outputs> 81 </outputs>
83 <tests> 82 <tests>
84 <test> 83 <test>
85 <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" />
86 <param name="skip_gene_tables" value="True" /> 108 <param name="skip_gene_tables" value="True" />
87 <param name="skip_gerp_bp" value="True" /> 109 <param name="skip_gerp_bp" value="True" />
88 <param name="skip_cadd" value="True" /> 110 <param name="skip_cadd" value="True" />
89 <param name="no_genotypes" value="True" /> 111 <param name="no_genotypes" value="True" />
90 <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" />
91 </test> 123 </test>
92 </tests> 124 </tests>
93 <help><![CDATA[ 125 <help><![CDATA[
94 **What it does** 126 **What it does**
95 127