Mercurial > repos > artbio > gatk4
changeset 1:b040adcfeefd draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
| author | artbio |
|---|---|
| date | Tue, 04 Jan 2022 15:10:59 +0000 |
| parents | c51c08cc9fcc |
| children | 646e6943bcd2 |
| files | MergeMutectStats.xml macros.xml test-data/chr1_stats.tsv test-data/chr2_stats.tsv test-data/chrM_stats.tsv test-data/merged_Mutect2_stats.tsv |
| diffstat | 6 files changed, 125 insertions(+), 1 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MergeMutectStats.xml Tue Jan 04 15:10:59 2022 +0000 @@ -0,0 +1,116 @@ +<tool id="mergemutectstats" name="gatk4 MergeMutectStats" version="@WRAPPER_VERSION@" profile="18.05"> + <description>Merge the stats output by scatters of a single Mutect2 job</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="version_cmd"/> + <command detect_errors="exit_code"> + <![CDATA[ + gatk MergeMutectStats + #for $file in $inputs: + --stats $file + #end for + --output $merge_stats + ]]> + </command> + <inputs> + <param name="inputs" type="data" format="tabular" label="stats files" multiple="true" + help="merge the stats files from multiple Mutect2 jobs"/> + </inputs> + <outputs> + <data format="tabular" name="merge_stats" label="Merged Mutect2 callable statistics" /> + </outputs> + <tests> + <test> + <param name="inputs" value="chr1_stats.tsv,chr2_stats.tsv,chrM_stats.tsv" ftype="tabular" /> + <output name="merge_stats" file="merged_Mutect2_stats.tsv" /> + </test> + </tests> + <help><![CDATA[ +Usage examples +~~~~~~~~~~~~~~ + + +:: + + gatk MergeMutectStats \ + + -stats unfiltered1.vcf.stats \ + + -stats unfiltered2.vcf.stats \ + + -O merged.stats + + +Mutect2 creates unfiltered.vcf.stats and FilterMutectCalls knows to look for it. However, +if you are scattering Mutect2 over multiple jobs you must merge the stats files with MergeMutectStats: + +Usage +~~~~~ + + +:: + + USAGE: MergeMutectStats [arguments] + + Merge the stats output by scatters of a single Mutect2 job + Version:4.1.7.0 + + + Required Arguments: + + --output,-O:File Output stats Required. + + --stats:File Stats from Mutect2 scatters of a single tumor or tumor-normal pair This argument must be + specified at least once. Required. + + + Optional Arguments: + + --arguments_file:File read one or more arguments files and add them to the command line This argument may be + specified 0 or more times. Default value: null. + + --gatk-config-file:String A configuration file to use with the GATK. Default value: null. + + --gcs-max-retries,-gcs-retries:Integer + If the GCS bucket channel errors out, how many times it will attempt to re-initiate the + connection Default value: 20. + + --gcs-project-for-requester-pays:String + Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be + accessed. Default value: . + + --help,-h:Boolean display the help message Default value: false. Possible values: {true, false} + + --QUIET:Boolean Whether to suppress job-summary info on System.err. Default value: false. Possible + values: {true, false} + + --tmp-dir:GATKPathSpecifier Temp directory to use. Default value: null. + + --use-jdk-deflater,-jdk-deflater:Boolean + Whether to use the JdkDeflater (as opposed to IntelDeflater) Default value: false. + Possible values: {true, false} + + --use-jdk-inflater,-jdk-inflater:Boolean + Whether to use the JdkInflater (as opposed to IntelInflater) Default value: false. + Possible values: {true, false} + + --verbosity,-verbosity:LogLevel + Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING, + INFO, DEBUG} + + --version:Boolean display the version number for this tool Default value: false. Possible values: {true, + false} + + + Advanced Arguments: + + --showHidden,-showHidden:Boolean + display hidden arguments Default value: false. Possible values: {true, false} + +]]></help> + <citations> + <expand macro="citations"/> + </citations> +</tool>
--- a/macros.xml Wed Dec 29 01:36:41 2021 +0000 +++ b/macros.xml Tue Jan 04 15:10:59 2022 +0000 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@VERSION@">4.1.7.0</token> - <token name="@WRAPPER_VERSION@">@VERSION@+galaxy1</token> + <token name="@WRAPPER_VERSION@">@VERSION@+galaxy2</token> <xml name="requirements"> <requirements>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chr1_stats.tsv Tue Jan 04 15:10:59 2022 +0000 @@ -0,0 +1,2 @@ +statistic value +callable 2.201717E8
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chr2_stats.tsv Tue Jan 04 15:10:59 2022 +0000 @@ -0,0 +1,2 @@ +statistic value +callable 2.34112388E8