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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
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2
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2 <description>Loading a VCF file into GEMINI</description>
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3 <expand macro="requirements" />
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4 <expand macro="version_command" />
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5 <macros>
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6 <import>gemini_macros.xml</import>
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7 <token name="@BINARY@">load</token>
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8 </macros>
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9 <command>
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10 <![CDATA[
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15
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11 ln -s "${ infile }" input.vcf &&
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12
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4
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13 gemini
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14 --annotation-dir ${annotation_databases.fields.path}
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4
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15 @BINARY@
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15
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16 -v input.vcf
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11
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17 #if str( $annotation_type ) != "None":
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18 -t $annotation_type
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19 #end if
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20
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21 #if $ped:
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22 -p $ped
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23 #end if
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24
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25 $skip_gerp_bp
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26 $skip_cadd
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27 $skip_gene_tables
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28 $no_load_genotypes
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29 $no_genotypes
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30 $passonly
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31 --cores \${GALAXY_SLOTS:-4}
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32
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33 "${ outfile }"
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34 ]]>
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35 </command>
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36 <expand macro="stdio" />
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37 <inputs>
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14
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38 <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.">
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39 <options>
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40 <filter type="add_value" value="hg19" />
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41 <filter type="add_value" value="Homo_sapiens_nuHg19_mtrCRS" />
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42 <filter type="add_value" value="hg_g1k_v37" />
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43 </options>
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44 </param>
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45
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46 <param name="annotation_type" type="select" label="The annotations to be used with the input vcf" help="(-t)">
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11
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47 <option value="None">None (not recommended)</option>
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48 <option value="snpEff" selected="True">snpEff annotated VCF file</option>
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49 <option value="VEP">VEP annotated VCF file</option>
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50 </param>
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51 <param name="ped" type="data" format="tablar" optional="True" label="Sample information file in PED+ format" help="(-p)" />
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4
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52 <expand macro="annotation_dir" />
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53
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54 <param name="skip_gerp_bp" type="boolean" truevalue="--skip-gerp-bp" falsevalue="" checked="False"
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55 label="Do not load GERP scores at base pair resolution" help="(--skip-gerp-bp)"/>
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56
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57 <param name="skip_cadd" type="boolean" truevalue="--skip-cadd" falsevalue="" checked="False"
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58 label="Do not load CADD scores" help="(--skip-cadd)"/>
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59
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60 <param name="skip_gene_tables" type="boolean" truevalue="--skip-gene-tables" falsevalue="" checked="False"
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61 label="Do not load gene tables" help="(--skip-gene-tables)"/>
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62
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63 <param name="no_load_genotypes" type="boolean" truevalue="--no-load-genotypes" falsevalue="" checked="False"
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64 label="Genotypes exist in the file, but should not be stored" help="(--no-load-genotypes)"/>
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65
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66 <param name="no_genotypes" type="boolean" truevalue="--no-load-genotypes" falsevalue="" checked="False"
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67 label="There are no genotypes in the file" help="e.g. some 1000G VCFs (--no-genotypes)"/>
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68
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69 <param name="passonly" type="boolean" truevalue="--passonly" falsevalue="" checked="False"
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70 label="Keep only variants that pass all filters" help="e.g. some 1000G VCFs (--passonly)"/>
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71
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72 </inputs>
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73 <outputs>
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11
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74 <data name="outfile" format="gemini.sqlite" />
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75 </outputs>
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76 <tests>
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77 <test>
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78 </test>
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79 </tests>
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80 <help>
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81 **What it does**
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82
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83 Before we can use GEMINI to explore genetic variation, we must first load our VCF file into the GEMINI database framework.
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84 We expect you to have first annotated the functional consequence of each variant in your VCF using either VEP or snpEff.
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85
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86 http://gemini.readthedocs.org/en/latest/content/loading.html
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87
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88 @CITATION@
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89 </help>
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90 <expand macro="citations"/>
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91 </tool>
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