Mercurial > repos > artbio > gatk4

annotate MergeMutectStats.xml @ 2:646e6943bcd2 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
author artbio
date Sun, 15 Oct 2023 12:06:24 +0000
parents b040adcfeefd
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
646e6943bcd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gatk4 commit 9c42369510cce59bf0dcb0edb440322d17b18339
artbio
parents: 1
diff changeset
1 <tool id="mergemutectstats" name="gatk4 MergeMutectStats" version="@WRAPPER_VERSION@" profile="21.01">
1
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
2 <description>Merge the stats output by scatters of a single Mutect2 job</description>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
3 <macros>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
4 <import>macros.xml</import>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
5 </macros>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
6 <expand macro="requirements"/>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
7 <expand macro="version_cmd"/>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
8 <command detect_errors="exit_code">
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
9 <![CDATA[
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
10 gatk MergeMutectStats
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
11 #for $file in $inputs:
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
12 --stats $file
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
13 #end for
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
14 --output $merge_stats
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
15 ]]>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
16 </command>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
17 <inputs>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
18 <param name="inputs" type="data" format="tabular" label="stats files" multiple="true"
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
19 help="merge the stats files from multiple Mutect2 jobs"/>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
20 </inputs>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
21 <outputs>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
22 <data format="tabular" name="merge_stats" label="Merged Mutect2 callable statistics" />
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
23 </outputs>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
24 <tests>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
25 <test>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
26 <param name="inputs" value="chr1_stats.tsv,chr2_stats.tsv,chrM_stats.tsv" ftype="tabular" />
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
27 <output name="merge_stats" file="merged_Mutect2_stats.tsv" />
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
28 </test>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
29 </tests>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
30 <help><![CDATA[
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
31 Usage examples
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
32 ~~~~~~~~~~~~~~
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
33
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
34
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
35 ::
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
36
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
37 gatk MergeMutectStats \
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
38
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
39 -stats unfiltered1.vcf.stats \
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
40
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
41 -stats unfiltered2.vcf.stats \
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
42
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
43 -O merged.stats
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
44
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
45
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
46 Mutect2 creates unfiltered.vcf.stats and FilterMutectCalls knows to look for it. However,
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
47 if you are scattering Mutect2 over multiple jobs you must merge the stats files with MergeMutectStats:
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
48
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
49 Usage
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
50 ~~~~~
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
51
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
52
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
53 ::
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
54
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
55 USAGE: MergeMutectStats [arguments]
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
56
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
57 Merge the stats output by scatters of a single Mutect2 job
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
58 Version:4.1.7.0
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
59
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
60
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
61 Required Arguments:
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
62
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
63 --output,-O:File Output stats Required.
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
64
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
65 --stats:File Stats from Mutect2 scatters of a single tumor or tumor-normal pair This argument must be
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
66 specified at least once. Required.
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
67
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
68
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
69 Optional Arguments:
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
70
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
71 --arguments_file:File read one or more arguments files and add them to the command line This argument may be
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
72 specified 0 or more times. Default value: null.
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
73
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
74 --gatk-config-file:String A configuration file to use with the GATK. Default value: null.
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
75
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
76 --gcs-max-retries,-gcs-retries:Integer
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
77 If the GCS bucket channel errors out, how many times it will attempt to re-initiate the
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
78 connection Default value: 20.
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
79
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
80 --gcs-project-for-requester-pays:String
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
81 Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
82 accessed. Default value: .
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
83
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
84 --help,-h:Boolean display the help message Default value: false. Possible values: {true, false}
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
85
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
86 --QUIET:Boolean Whether to suppress job-summary info on System.err. Default value: false. Possible
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
87 values: {true, false}
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
88
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
89 --tmp-dir:GATKPathSpecifier Temp directory to use. Default value: null.
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
90
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
91 --use-jdk-deflater,-jdk-deflater:Boolean
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
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"
artbio
parents:
diff changeset
93 Possible values: {true, false}
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
94
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
95 --use-jdk-inflater,-jdk-inflater:Boolean
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
96 Whether to use the JdkInflater (as opposed to IntelInflater) Default value: false.
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
97 Possible values: {true, false}
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
98
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
99 --verbosity,-verbosity:LogLevel
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
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"
artbio
parents:
diff changeset
101 INFO, DEBUG}
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
102
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
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"
artbio
parents:
diff changeset
104 false}
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
105
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
106
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
107 Advanced Arguments:
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
108
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
109 --showHidden,-showHidden:Boolean
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
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"
artbio
parents:
diff changeset
111
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
112 ]]></help>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
113 <citations>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
114 <expand macro="citations"/>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
115 </citations>
b040adcfeefd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gatk4 commit f2a0b974cb707179f090dec550d219ff3cb1af29"
artbio
parents:
diff changeset
116 </tool>