Mercurial > repos > iuc > gemini_load

annotate gemini_load.xml @ 3:cf61daf064fe draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 1f7418d74c6fcd61a050106ca5f9b66ab9a4c33d
author iuc
date Wed, 17 Oct 2018 13:25:58 -0400
parents 269c40fdcccb
children 5c5cdbdc3534
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269c40fdcccb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.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[
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12 ln -s "${ infile }" input.vcf &&
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13 bgzip -c input.vcf > input.vcf.gz &&
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14 tabix -p vcf input.vcf.gz &&
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16 gemini
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17 #if $annotation_databases:
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18 --annotation-dir "${annotation_databases.fields.path}"
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19 #end if
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20 @BINARY@
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21 -v input.vcf.gz
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22 #if str( $annotation_type ) != "None":
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23 -t "$annotation_type"
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24 #end if
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25
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26 #if $ped:
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27 -p $ped
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28 #end if
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29
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30 $skip_gerp_bp
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31 $skip_cadd
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32 $skip_gene_tables
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33 $no_load_genotypes
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34 $no_genotypes
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35 $passonly
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36 $infostring
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37 --cores \${GALAXY_SLOTS:-4}
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38
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39 "${ outfile }"
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40 ]]>
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41 </command>
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42 <inputs>
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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.">
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44 <options>
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45 <filter type="add_value" value="hg19" />
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46 <filter type="add_value" value="Homo_sapiens_nuHg19_mtrCRS" />
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47 <filter type="add_value" value="hg_g1k_v37" />
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48 </options>
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49 </param>
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50
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51 <param name="annotation_type" type="select" label="The annotations to be used with the input vcf" help="(-t)">
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52 <option value="None">None (not recommended)</option>
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53 <option value="snpEff" selected="True">snpEff annotated VCF file</option>
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54 <option value="VEP">VEP annotated VCF file</option>
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55 </param>
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56 <param name="ped" type="data" format="tabular" optional="True" label="Sample information file in PED+ format" help="(-p)" />
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57 <expand macro="annotation_dir" />
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58
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59 <param name="skip_gerp_bp" type="boolean" truevalue="--skip-gerp-bp" falsevalue="" checked="False"
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60 label="Do not load GERP scores at base pair resolution" help="(--skip-gerp-bp)"/>
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61
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62 <param name="skip_cadd" type="boolean" truevalue="--skip-cadd" falsevalue="" checked="False"
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63 label="Do not load CADD scores" help="(--skip-cadd)"/>
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64
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65 <param name="skip_gene_tables" type="boolean" truevalue="--skip-gene-tables" falsevalue="" checked="False"
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66 label="Do not load gene tables" help="(--skip-gene-tables)"/>
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67
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68 <param name="no_load_genotypes" type="boolean" truevalue="--no-load-genotypes" falsevalue="" checked="False"
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69 label="Genotypes exist in the file, but should not be stored" help="(--no-load-genotypes)"/>
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70
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71 <param name="no_genotypes" type="boolean" truevalue="--no-genotypes" falsevalue="" checked="False"
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72 label="There are no genotypes in the file" help="e.g. some 1000G VCFs (--no-genotypes)"/>
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73
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74 <param name="passonly" type="boolean" truevalue="--passonly" falsevalue="" checked="False"
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75 label="Keep only variants that pass all filters" help="e.g. some 1000G VCFs (--passonly)"/>
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76
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77 <param name="infostring" type="boolean" truevalue="--save-info-string" falsevalue="" checked="False"
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78 label="Load INFO string from VCF file" help="(--save-info-string)"/>
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79 </inputs>
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80 <outputs>
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81 <data name="outfile" format="gemini.sqlite" />
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82 </outputs>
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83 <tests>
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84 <test>
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85 <param name="infile" value="gemini_load_input.vcf" ftype="vcf" />
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86 <param name="skip_gene_tables" value="True" />
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87 <param name="skip_gerp_bp" value="True" />
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88 <param name="skip_cadd" value="True" />
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89 <param name="no_genotypes" value="True" />
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90 <output name="outfile" file="gemini_load_result.db" compare="sim_size" delta="1000"/>
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91 </test>
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92 </tests>
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93 <help><![CDATA[
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94 **What it does**
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95
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96 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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97 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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98
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99 ]]></help>
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100 <expand macro="citations"/>
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101 </tool>