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comparison 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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0:c51c08cc9fcc 1:b040adcfeefd
1 <tool id="mergemutectstats" name="gatk4 MergeMutectStats" version="@WRAPPER_VERSION@" profile="18.05">
2 <description>Merge the stats output by scatters of a single Mutect2 job</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_cmd"/>
8 <command detect_errors="exit_code">
9 <![CDATA[
10 gatk MergeMutectStats
11 #for $file in $inputs:
12 --stats $file
13 #end for
14 --output $merge_stats
15 ]]>
16 </command>
17 <inputs>
18 <param name="inputs" type="data" format="tabular" label="stats files" multiple="true"
19 help="merge the stats files from multiple Mutect2 jobs"/>
20 </inputs>
21 <outputs>
22 <data format="tabular" name="merge_stats" label="Merged Mutect2 callable statistics" />
23 </outputs>
24 <tests>
25 <test>
26 <param name="inputs" value="chr1_stats.tsv,chr2_stats.tsv,chrM_stats.tsv" ftype="tabular" />
27 <output name="merge_stats" file="merged_Mutect2_stats.tsv" />
28 </test>
29 </tests>
30 <help><![CDATA[
31 Usage examples
32 ~~~~~~~~~~~~~~
33
34
35 ::
36
37 gatk MergeMutectStats \
38
39 -stats unfiltered1.vcf.stats \
40
41 -stats unfiltered2.vcf.stats \
42
43 -O merged.stats
44
45
46 Mutect2 creates unfiltered.vcf.stats and FilterMutectCalls knows to look for it. However,
47 if you are scattering Mutect2 over multiple jobs you must merge the stats files with MergeMutectStats:
48
49 Usage
50 ~~~~~
51
52
53 ::
54
55 USAGE: MergeMutectStats [arguments]
56
57 Merge the stats output by scatters of a single Mutect2 job
58 Version:4.1.7.0
59
60
61 Required Arguments:
62
63 --output,-O:File Output stats Required.
64
65 --stats:File Stats from Mutect2 scatters of a single tumor or tumor-normal pair This argument must be
66 specified at least once. Required.
67
68
69 Optional Arguments:
70
71 --arguments_file:File read one or more arguments files and add them to the command line This argument may be
72 specified 0 or more times. Default value: null.
73
74 --gatk-config-file:String A configuration file to use with the GATK. Default value: null.
75
76 --gcs-max-retries,-gcs-retries:Integer
77 If the GCS bucket channel errors out, how many times it will attempt to re-initiate the
78 connection Default value: 20.
79
80 --gcs-project-for-requester-pays:String
81 Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be
82 accessed. Default value: .
83
84 --help,-h:Boolean display the help message Default value: false. Possible values: {true, false}
85
86 --QUIET:Boolean Whether to suppress job-summary info on System.err. Default value: false. Possible
87 values: {true, false}
88
89 --tmp-dir:GATKPathSpecifier Temp directory to use. Default value: null.
90
91 --use-jdk-deflater,-jdk-deflater:Boolean
92 Whether to use the JdkDeflater (as opposed to IntelDeflater) Default value: false.
93 Possible values: {true, false}
94
95 --use-jdk-inflater,-jdk-inflater:Boolean
96 Whether to use the JdkInflater (as opposed to IntelInflater) Default value: false.
97 Possible values: {true, false}
98
99 --verbosity,-verbosity:LogLevel
100 Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING,
101 INFO, DEBUG}
102
103 --version:Boolean display the version number for this tool Default value: false. Possible values: {true,
104 false}
105
106
107 Advanced Arguments:
108
109 --showHidden,-showHidden:Boolean
110 display hidden arguments Default value: false. Possible values: {true, false}
111
112 ]]></help>
113 <citations>
114 <expand macro="citations"/>
115 </citations>
116 </tool>