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1 <tool id="covacs_ApplyRecalibrator" name="covacs_ApplyRecalibrator" version="3.8">
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2 <description>gatk ApplyRecalibrator wrapper for covacs</description>
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3 <macros>
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4 <import>bed_macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="3.8" >gatk</requirement>
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8 </requirements>
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9 <command>
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10 <![CDATA[
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11 ### call the .sh to untar the package
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12 bash $__tool_directory__/mv_untar_gatk.sh &> $log &&
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13
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14
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15
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16 #if $bed_source.bed_source_selector == "history" and $bed_source.bed_history
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17 ln -s $bed_source.bed_history region.bed &&
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18 #end if
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19
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20 ln -s $input1 input1.vcf &&
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21
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22 java -jar \$CONDA_PREFIX/../../GenomeAnalysisTK.jar -T ApplyRecalibration
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23
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24
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25
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26 #if $bed_source.bed_source_selector == "history" and $bed_source.bed_history
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27 -L region.bed
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28 #end if
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29 #if $bed_source.bed_source_selector == "cached"
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30 -L $bed_source.bed_cached.fields.path
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31 #end if
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32
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33
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34 -ip $ip
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35 ###index from .loc
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36 -R $ref_file.fields.path
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37
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38 -input input1.vcf
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39 --ts_filter_level $ts_filter_level
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40 -tranchesFile $input2
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41 -recalFile $input3
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42 -mode $mode
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43 -ef -o variants_recal.filtered.98HQ.vcf 2> $log
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44
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45
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46
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47
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48 ]]>
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49 </command>
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50 <inputs>
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51 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
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52 <options from_data_table="covacs_gatk_indexes">
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53 <filter type="sort_by" column="2" />
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54 <validator type="no_options" message="No indexes are available" />
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55 </options>
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56 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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57 </param>
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58 <param format="vcf" name="input1" label="input vcf" type="data" optional="true" />
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59 <expand macro="bed_loc"/>
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60 <param name="ip" type="integer" value="100" help="Amount of padding (in bp) to add to each interval"/>
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61 <param name="ts_filter_level" type="float" value="99.5" help="The truth sensitivity level at which to start filtering"/>
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62 <param name="input2" type="data" label="tranchesfile" help="tranches file from VariantRecalibrator"/>
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63 <param name="input3" type="data" label="recalfile" help="tranches file from VariantRecalibrator"/>
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64 <param name="mode" type="select" help="Recalibration mode to employ: SNP for recalibrating only SNPs, INDEL for indels">
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65 <option value="SNP">snp</option>
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66 <option value="INDEL">INDEL</option>
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67 </param>
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68 </inputs>
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69 <outputs>
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70 <data format="vcf" name="variants_recal" from_work_dir="variants_recal.filtered.98HQ.vcf" label="${tool.name} on ${on_string}:recal_filtered"/>
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71 <data format="txt" name="log" label="${tool.name} on ${on_string}:log"/>
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72 </outputs>
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73 <help>
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74 .. class:: warningmark
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75
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76 **IMPORTANT** to get the wrapper ready to start the admin user have to download gatk GATK version 3.8 from the broadinstitute site https://software.broadinstitute.org/gatk/download/archive and then move it in the conda_prefix folder, the path of the conda_prefix is written in the galaxy.ini(or .yml) file
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77
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78 **more informations** at https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_variantrecalibration_ApplyRecalibration.php
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79
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80 -----
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81
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82 **implemented options** ApplyRecalibrator:
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83
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84 **-L** : One or more genomic intervals over which to operate(file.bed)
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85
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86 **-ip** : Amount of padding (in bp) to add to each interval
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87
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88 **-R** : Reference sequence file
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89
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90 **-ts\_filter_\level** : The truth sensitivity level at which to start filtering
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91
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92 **-tranchesFile** : Level of sensitivity. A tranchesfile is required. Please read the GATK manual if you do according to the input tranches file
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93
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94 **-recallFile** : The input recal file used by ApplyRecalibration
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95
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96 **-mode** : Recalibration mode to employ: SNP for recalibrating only SNPs, INDEL for indels
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97
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98 </help>
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99 <citations>
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100 <citation type="doi">10.1186/s12864-018-4508-1</citation>
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101 </citations>
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102 </tool>
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103
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