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annotate MergeMutectStats.xml @ 1:b040adcfeefd draft

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"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
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b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
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1 <tool id="mergemutectstats" name="gatk4 MergeMutectStats" version="@WRAPPER_VERSION@" profile="18.05">
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2 <description>Merge the stats output by scatters of a single Mutect2 job</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_cmd"/>
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8 <command detect_errors="exit_code">
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9 <![CDATA[
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
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10 gatk MergeMutectStats
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11 #for $file in $inputs:
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12 --stats $file
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13 #end for
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14 --output $merge_stats
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15 ]]>
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16 </command>
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17 <inputs>
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18 <param name="inputs" type="data" format="tabular" label="stats files" multiple="true"
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19 help="merge the stats files from multiple Mutect2 jobs"/>
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20 </inputs>
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21 <outputs>
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22 <data format="tabular" name="merge_stats" label="Merged Mutect2 callable statistics" />
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="inputs" value="chr1_stats.tsv,chr2_stats.tsv,chrM_stats.tsv" ftype="tabular" />
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27 <output name="merge_stats" file="merged_Mutect2_stats.tsv" />
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28 </test>
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29 </tests>
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30 <help><![CDATA[
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31 Usage examples
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32 ~~~~~~~~~~~~~~
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35 ::
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37 gatk MergeMutectStats \
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39 -stats unfiltered1.vcf.stats \
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41 -stats unfiltered2.vcf.stats \
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43 -O merged.stats
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46 Mutect2 creates unfiltered.vcf.stats and FilterMutectCalls knows to look for it. However,
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47 if you are scattering Mutect2 over multiple jobs you must merge the stats files with MergeMutectStats:
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48
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49 Usage
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50 ~~~~~
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53 ::
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55 USAGE: MergeMutectStats [arguments]
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57 Merge the stats output by scatters of a single Mutect2 job
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58 Version:4.1.7.0
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59
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61 Required Arguments:
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63 --output,-O:File Output stats Required.
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64
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65 --stats:File Stats from Mutect2 scatters of a single tumor or tumor-normal pair This argument must be
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66 specified at least once. Required.
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67
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68
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69 Optional Arguments:
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71 --arguments_file:File read one or more arguments files and add them to the command line This argument may be
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72 specified 0 or more times. Default value: null.
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74 --gatk-config-file:String A configuration file to use with the GATK. Default value: null.
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76 --gcs-max-retries,-gcs-retries:Integer
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77 If the GCS bucket channel errors out, how many times it will attempt to re-initiate the
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78 connection Default value: 20.
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80 --gcs-project-for-requester-pays:String
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81 Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be
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82 accessed. Default value: .
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83
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84 --help,-h:Boolean display the help message Default value: false. Possible values: {true, false}
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85
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86 --QUIET:Boolean Whether to suppress job-summary info on System.err. Default value: false. Possible
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87 values: {true, false}
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88
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89 --tmp-dir:GATKPathSpecifier Temp directory to use. Default value: null.
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91 --use-jdk-deflater,-jdk-deflater:Boolean
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92 Whether to use the JdkDeflater (as opposed to IntelDeflater) Default value: false.
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
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93 Possible values: {true, false}
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
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94
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
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95 --use-jdk-inflater,-jdk-inflater:Boolean
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
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96 Whether to use the JdkInflater (as opposed to IntelInflater) Default value: false.
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97 Possible values: {true, false}
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
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98
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
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99 --verbosity,-verbosity:LogLevel
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
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100 Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING,
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
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101 INFO, DEBUG}
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
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102
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
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103 --version:Boolean display the version number for this tool Default value: false. Possible values: {true,
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
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104 false}
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
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105
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
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106
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
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107 Advanced Arguments:
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
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108
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109 --showHidden,-showHidden:Boolean
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
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110 display hidden arguments Default value: false. Possible values: {true, false}
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
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111
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112 ]]></help>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
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113 <citations>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
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114 <expand macro="citations"/>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
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115 </citations>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
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116 </tool>