Mercurial > repos > iuc > gemini_load

comparison gemini_load.xml @ 0:7f7fbd50e9dc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit e88029bb12e5262687267293f9d2a694eb00d3f0-dirty
author iuc
date Tue, 29 Dec 2015 10:22:13 -0500
parents
children 386b3e7c2f77
comparison
equal deleted inserted replaced
-1:000000000000 0:7f7fbd50e9dc
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
2 <description>Loading a VCF file into GEMINI</description>
3 <macros>
4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">load</token>
6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <expand macro="version_command" />
10 <command>
11 <![CDATA[
12 ln -s "${ infile }" input.vcf &&
13 bgzip -c input.vcf > input.vcf.gz &&
14 tabix -p vcf input.vcf.gz &&
15
16 gemini
17 #if $annotation_databases:
18 --annotation-dir ${annotation_databases.fields.path}
19 #end if
20 @BINARY@
21 -v input.vcf.gz
22 #if str( $annotation_type ) != "None":
23 -t $annotation_type
24 #end if
25
26 #if $ped:
27 -p $ped
28 #end if
29
30 $skip_gerp_bp
31 $skip_cadd
32 $skip_gene_tables
33 $no_load_genotypes
34 $no_genotypes
35 $passonly
36 $infostring
37 --cores \${GALAXY_SLOTS:-4}
38
39 "${ outfile }"
40 ]]>
41 </command>
42 <inputs>
43 <param name="infile" type="data" format="vcf" label="VCF file to be loaded in the GEMINI database" help="Only build 37 (aka hg19) of the human genome is supported.">
44 <options>
45 <filter type="add_value" value="hg19" />
46 <filter type="add_value" value="Homo_sapiens_nuHg19_mtrCRS" />
47 <filter type="add_value" value="hg_g1k_v37" />
48 </options>
49 </param>
50
51 <param name="annotation_type" type="select" label="The annotations to be used with the input vcf" help="(-t)">
52 <option value="None">None (not recommended)</option>
53 <option value="snpEff" selected="True">snpEff annotated VCF file</option>
54 <option value="VEP">VEP annotated VCF file</option>
55 </param>
56 <param name="ped" type="data" format="tabular" optional="True" label="Sample information file in PED+ format" help="(-p)" />
57 <expand macro="annotation_dir" />
58
59 <param name="skip_gerp_bp" type="boolean" truevalue="--skip-gerp-bp" falsevalue="" checked="False"
60 label="Do not load GERP scores at base pair resolution" help="(--skip-gerp-bp)"/>
61
62 <param name="skip_cadd" type="boolean" truevalue="--skip-cadd" falsevalue="" checked="False"
63 label="Do not load CADD scores" help="(--skip-cadd)"/>
64
65 <param name="skip_gene_tables" type="boolean" truevalue="--skip-gene-tables" falsevalue="" checked="False"
66 label="Do not load gene tables" help="(--skip-gene-tables)"/>
67
68 <param name="no_load_genotypes" type="boolean" truevalue="--no-load-genotypes" falsevalue="" checked="False"
69 label="Genotypes exist in the file, but should not be stored" help="(--no-load-genotypes)"/>
70
71 <param name="no_genotypes" type="boolean" truevalue="--no-genotypes" falsevalue="" checked="False"
72 label="There are no genotypes in the file" help="e.g. some 1000G VCFs (--no-genotypes)"/>
73
74 <param name="passonly" type="boolean" truevalue="--passonly" falsevalue="" checked="False"
75 label="Keep only variants that pass all filters" help="e.g. some 1000G VCFs (--passonly)"/>
76
77 <param name="infostring" type="boolean" truevalue="--save-info-string" falsevalue="" checked="False"
78 label="Load INFO string from VCF file" help="(--save-info-string)"/>
79 </inputs>
80 <outputs>
81 <data name="outfile" format="gemini.sqlite" />
82 </outputs>
83 <tests>
84 <test>
85 <param name="infile" value="gemini_load_input.vcf" ftype="vcf" />
86 <param name="skip_gene_tables" value="True" />
87 <param name="skip_gerp_bp" value="True" />
88 <param name="skip_cadd" value="True" />
89 <param name="no_genotypes" value="True" />
90 <output name="outfile" file="gemini_load_result.db" compare="sim_size" delta="1000"/>
91 </test>
92 </tests>
93 <help><![CDATA[
94 **What it does**
95
96 Before we can use GEMINI to explore genetic variation, we must first load our VCF file into the GEMINI database framework.
97 We expect you to have first annotated the functional consequence of each variant in your VCF using either VEP or snpEff.
98
99 ]]></help>
100 <expand macro="citations"/>
101 </tool>