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1 <tool id="covacs_Select_Filtration" name="covacs_Select_filtration" version="3.8">
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2 <description>SelectVariants VariantFiltration wrapper for covacs, use in case of not enough snp or indels error in covacs_VariantRecalibrator</description>
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3 <macros>
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4 </macros>
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5 <requirements>
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6 <requirement type="package" version="3.8" >gatk</requirement>
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7 </requirements>
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8 <command>
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9 <![CDATA[
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10 ### call the .sh to untar the package
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11 bash $__tool_directory__/mv_untar_gatk.sh &> $log &&
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12
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13 ##sym link to run GATK
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14
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15 ln -s $input1 input1.vcf &&
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16
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17 ##GATK tool call
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18 java -jar \$CONDA_PREFIX/../../GenomeAnalysisTK.jar
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19 -T SelectVariants
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20 -R $ref_file.fields.path
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21 -V input1.vcf
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22 -selectType $TYPE
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23 -o variants_recal.indels.vcf 2>$log
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24 &&
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25 java -jar \$CONDA_PREFIX/../../GenomeAnalysisTK.jar
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26 -T VariantFiltration
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27 -R $ref_file.fields.path
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28 -V variants_recal.indels.vcf
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29 --filterExpression "DP<8 || QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0"
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30 --filterName "filter_LQ_$TYPE"
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31 -o variants_recal.filtered.small.panel.region.vcf
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32
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33 2>> $log
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34 ]]>
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35 </command>
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36 <inputs>
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37 <param format="vcf" name="input1" label="input VCF" type="data" optional="true" />
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38 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
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39 <options from_data_table="covacs_gatk_indexes">
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40 <filter type="sort_by" column="2" />
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41 <validator type="no_options" message="No indexes are available" />
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42 </options>
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43 <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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44 </param>
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45 <param name="TYPE" type="select" optional="true">
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46 <option value="INDEL">INDEL</option>
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47 <option value="SNP" selected="true" >SNP</option>
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48 </param>
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49 </inputs>
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50 <outputs>
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51 <data format="vcf" name="recal" from_work_dir="variants_recal.indels.vcf" label="SelectVariants on ${on_string} $TYPE :recal"/>
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52 <data format="vcf" name="filtered" from_work_dir="variants_recal.filtered.small.panel.region.vcf" label="VariantFiltration on ${on_string} $TYPE :recal"/>
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53 <data format="txt" name="log" label="log"/>
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54 </outputs>
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55 <help>
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56 **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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57
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58 **more informations** at https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php , https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_filters_VariantFiltration.php
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59
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60 **Implemented options** SelectVariants <![CDATA[ &]]> VariantFiltration
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61
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62 -R Reference sequence file
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63
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64 -V vcf input
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65
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66 other options are fixed based on covacs pipeline
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67
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68 **description** this step can be used if covacs_indel_snp have not enough data to create the model, it calls SelectVariants and VariantFiltration applying the filter expression --filterExpression <![CDATA["DP<8 || QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0"]]> to filter the variants both snp and indels
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69
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70 </help>
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71 <citations>
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72 <citation type="doi">10.1186/s12864-018-4508-1</citation>
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73 </citations>
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74 </tool>
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75
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