Mercurial > repos > elixir-it > covacs_apply_recalibrator
changeset 0:c785cec34cdc draft
Uploaded
author | elixir-it |
---|---|
date | Fri, 09 Nov 2018 05:27:39 -0500 |
parents | |
children | 48dc4c9bc497 |
files | bed_macros.xml covacs_ApplyRecalibrator.xml mv_untar_gatk.sh tool-data/covacs_bed.loc.sample tool-data/covacs_gatk_indexes.loc.sample tool_data_table_conf.xml.sample |
diffstat | 6 files changed, 199 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bed_macros.xml Fri Nov 09 05:27:39 2018 -0500 @@ -0,0 +1,22 @@ +<macros> + <macro name="bed_loc"> + <conditional name="bed_source"> + <param name="bed_source_selector" type="select" label="Will you select a bed file from your history or use a built-in bed?" optional="true"> + <option value="cached">Use a built-in bed</option> + <option value="history">Use a bed from history as reference</option> + </param> + <when value="cached"> + <param name="bed_cached" type="select" label="Using reference bed" help="Select bed from the list"> + <options from_data_table="covacs_bed"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No bed are available" /> + </options> + <validator type="no_options" message="A built-in bed file is not available"/> + </param> + </when> + <when value="history"> + <param name="bed_history" type="data" format="bed" label="Use the following dataset as reference bed " help="You can upload a bed file to the history and use it" optional="true" /> + </when> + </conditional> + </macro> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/covacs_ApplyRecalibrator.xml Fri Nov 09 05:27:39 2018 -0500 @@ -0,0 +1,103 @@ + <tool id="covacs_ApplyRecalibrator" name="covacs_ApplyRecalibrator" version="3.8"> + <description>gatk ApplyRecalibrator wrapper </description> + <macros> + <import>bed_macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="3.8" >gatk</requirement> + </requirements> + <command> + <![CDATA[ + ### call the .sh to untar the package + sh $__tool_directory__/mv_untar_gatk.sh && + + + + #if $bed_source.bed_source_selector == "history" and $bed_source.bed_history + ln -s $bed_source.bed_history region.bed && + #end if + + ln -s $input1 input1.vcf && + + java -jar \$CONDA_PREFIX/../../GenomeAnalysisTK.jar -T ApplyRecalibration + + + + #if $bed_source.bed_source_selector == "history" and $bed_source.bed_history + -L region.bed + #end if + #if $bed_source.bed_source_selector == "cached" + -L $bed_source.bed_cached.fields.path + #end if + + + -ip $ip + ###index from .loc + -R $ref_file.fields.path + + -input input1.vcf + --ts_filter_level $ts_filter_level + -tranchesFile $input2 + -recalFile $input3 + -mode $mode + -ef -o variants_recal.filtered.98HQ.vcf 2> $log + + + + + ]]> + </command> + <inputs> + <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list"> + <options from_data_table="covacs_gatk_indexes"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No indexes are available" /> + </options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + <param format="vcf" name="input1" label="input vcf" type="data" optional="true" /> + <expand macro="bed_loc"/> + <param name="ip" type="integer" value="100" help="Amount of padding (in bp) to add to each interval"/> + <param name="ts_filter_level" type="float" value="99.5" help="The truth sensitivity level at which to start filtering"/> + <param name="input2" type="data" label="tranchesfile" help="tranches file from VariantRecalibrator"/> + <param name="input3" type="data" label="recalfile" help="tranches file from VariantRecalibrator"/> + <param name="mode" type="select" help="Recalibration mode to employ: SNP for recalibrating only SNPs, INDEL for indels"> + <option value="SNP">snp</option> + <option value="INDEL">INDEL</option> + </param> + </inputs> + <outputs> + <data format="vcf" name="variants_recal" from_work_dir="variants_recal.filtered.98HQ.vcf" label="${tool.name} on ${on_string}:recal_filtered"/> + <data format="txt" name="log" label="${tool.name} on ${on_string}:log"/> + </outputs> + <help> +.. class:: warningmark + +**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 + + **more informations** at https://software.broadinstitute.org/gatk/documentation/tooldocs/3.8-0/org_broadinstitute_gatk_tools_walkers_variantrecalibration_ApplyRecalibration.php + +----- + +**implemented options** ApplyRecalibrator: + +**-L** : One or more genomic intervals over which to operate(file.bed) + +**-ip** : Amount of padding (in bp) to add to each interval + +**-R** : Reference sequence file + +**-ts\_filter_\level** : The truth sensitivity level at which to start filtering + +**-tranchesFile** : Level of sensitivity. A tranchesfile is required. Please read the GATK manual if you do according to the input tranches file + +**-recallFile** : The input recal file used by ApplyRecalibration + +**-mode** : Recalibration mode to employ: SNP for recalibrating only SNPs, INDEL for indels + + </help> + <citations> + <citation type="doi">10.1186/s12864-018-4508-1</citation> + </citations> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mv_untar_gatk.sh Fri Nov 09 05:27:39 2018 -0500 @@ -0,0 +1,9 @@ +#!/bin/bash +#if the .jar file is not present in the conda_prefix the script search the tar.gz in the conda_prefix of the vm +#and untar the archive +if [[ ! -f $CONDA_PREFIX/../../GenomeAnalysisTK.jar ]] ; then + tar -zxvf $CONDA_PREFIX/../../GenomeAnalysis*.tar.gz -C $CONDA_PREFIX/../../ + +else + echo GATK is present +fi
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/covacs_bed.loc.sample Fri Nov 09 05:27:39 2018 -0500 @@ -0,0 +1,17 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory bed file for covacs sequences data files. You will need +#to create these data files and then create a bed_loc.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bed_loc.loc +#file has this format (longer white space characters are TAB characters): +# +#<unique_id> <dbkey> <display_name> <file_path> +# +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. That is why the +#hg19 entry above looks odd. New genomes can be better-looking. +# +hg19 hg19 hg19-padded /export/BED/S07084713_Padded.bed +hgbed hg19 hg19-bed-test /export/BED/chr22.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/covacs_gatk_indexes.loc.sample Fri Nov 09 05:27:39 2018 -0500 @@ -0,0 +1,36 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of all covacs wrapper that need a gatk reference. You will need +#to create these data files and then create a covacs_gatk_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The covacs_gatk_indexes.loc +#file has this format (longer white space characters are TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, for example, if you had phiX indexed stored in +#/depot/data2/galaxy/phiX/base/, +#then the bwa_index.loc entry would look like this: +# +#phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa +# +#and your /depot/data2/galaxy/phiX/base/ directory +#would contain phiX.dict, phiX.fa.fai files. +# +# +#Your covacs_gatk_indexes.loc file should include an entry per line for each +#index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. For example: +# +#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa +#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa +#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa +#...etc... +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. That is why the +#hg19 entry above looks odd. New genomes can be better-looking. +# +hg38 hg38 hg38_GDC /export/gatkhg38pl/GRCh38.d1.vd1.fa +hg19 hg19 hg19 /export/gatk_hg19_index_bundle/ucsc.hg19.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Nov 09 05:27:39 2018 -0500 @@ -0,0 +1,12 @@ +<tables> +<!-- Location of bed-file for covacs --> + <table name="covacs_bed" comment_char="#"> + <columns> value, dbkey, name, path</columns> + <file path="tool-data/covacs_bed.loc" /> + </table> +<!-- Location of index file for covacs gatk wrapper --> + <table name="covacs_gatk_indexes" comment_char="#"> + <columns> value, dbkey, name, path</columns> + <file path="tool-data/covacs_gatk_indexes.loc" /> + </table> +</tables>