Mercurial > repos > iuc > gemini_load

annotate gemini_load.xml @ 4:264f4601dd1d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
author iuc
date Fri, 07 Dec 2018 12:51:01 -0500
parents 3ac6d0e85e98
children b382ddaf8445
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
0
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2 <description>Loading a VCF file into GEMINI</description>
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3 <macros>
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4 <import>gemini_macros.xml</import>
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5 <token name="@BINARY@">load</token>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command>
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11 <![CDATA[
4
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12 @PROVIDE_ANNO_DATA@
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13
0
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14 ln -s "${ infile }" input.vcf &&
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15 bgzip -c input.vcf > input.vcf.gz &&
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16 tabix -p vcf input.vcf.gz &&
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18 gemini
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19 @BINARY@
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20 -v input.vcf.gz
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21 #if str( $annotation_type ) != "None":
2
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22 -t "$annotation_type"
0
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23 #end if
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25 #if $ped:
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26 -p $ped
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27 #end if
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29 $skip_gerp_bp
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30 $skip_cadd
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31 $skip_gene_tables
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32 $no_load_genotypes
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33 $no_genotypes
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34 $passonly
3
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35 $infostring
0
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36 --cores \${GALAXY_SLOTS:-4}
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37
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38 "${ outfile }"
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39 ]]>
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40 </command>
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41 <inputs>
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42 <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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43 <options>
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44 <filter type="add_value" value="hg19" />
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45 <filter type="add_value" value="Homo_sapiens_nuHg19_mtrCRS" />
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46 <filter type="add_value" value="hg_g1k_v37" />
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47 </options>
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48 </param>
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49
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50 <param name="annotation_type" type="select" label="The annotations to be used with the input vcf" help="(-t)">
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51 <option value="None">None (not recommended)</option>
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52 <option value="snpEff" selected="True">snpEff annotated VCF file</option>
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53 <option value="VEP">VEP annotated VCF file</option>
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54 </param>
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55 <param name="ped" type="data" format="tabular" optional="True" label="Sample information file in PED+ format" help="(-p)" />
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56 <expand macro="annotation_dir" />
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57
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58 <param name="skip_gerp_bp" type="boolean" truevalue="--skip-gerp-bp" falsevalue="" checked="False"
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59 label="Do not load GERP scores at base pair resolution" help="(--skip-gerp-bp)"/>
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60
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61 <param name="skip_cadd" type="boolean" truevalue="--skip-cadd" falsevalue="" checked="False"
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62 label="Do not load CADD scores" help="(--skip-cadd)"/>
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63
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64 <param name="skip_gene_tables" type="boolean" truevalue="--skip-gene-tables" falsevalue="" checked="False"
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65 label="Do not load gene tables" help="(--skip-gene-tables)"/>
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66
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67 <param name="no_load_genotypes" type="boolean" truevalue="--no-load-genotypes" falsevalue="" checked="False"
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68 label="Genotypes exist in the file, but should not be stored" help="(--no-load-genotypes)"/>
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69
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70 <param name="no_genotypes" type="boolean" truevalue="--no-genotypes" falsevalue="" checked="False"
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71 label="There are no genotypes in the file" help="e.g. some 1000G VCFs (--no-genotypes)"/>
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72
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73 <param name="passonly" type="boolean" truevalue="--passonly" falsevalue="" checked="False"
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74 label="Keep only variants that pass all filters" help="e.g. some 1000G VCFs (--passonly)"/>
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75
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76 <param name="infostring" type="boolean" truevalue="--save-info-string" falsevalue="" checked="False"
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77 label="Load INFO string from VCF file" help="(--save-info-string)"/>
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78 </inputs>
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79 <outputs>
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80 <data name="outfile" format="gemini.sqlite" />
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81 </outputs>
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82 <tests>
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83 <test>
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84 <param name="infile" value="gemini_load_input.vcf" ftype="vcf" />
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85 <param name="skip_gene_tables" value="True" />
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86 <param name="skip_gerp_bp" value="True" />
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87 <param name="skip_cadd" value="True" />
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88 <param name="no_genotypes" value="True" />
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89 <output name="outfile" file="gemini_load_result.db" compare="sim_size" delta="1000"/>
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90 </test>
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91 </tests>
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92 <help><![CDATA[
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93 **What it does**
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94
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95 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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96 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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97
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98 ]]></help>
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99 <expand macro="citations"/>
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100 </tool>