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biopet.biopet
Commits
acd85018
Commit
acd85018
authored
Jul 05, 2016
by
Moustakas
Browse files
Improve user documentation for the tool
parent
86c0fea2
Changes
1
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
View file @
acd85018
...
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@@ -52,22 +52,22 @@ object AnnotateVcfWithBed extends ToolCommand {
class
OptParser
extends
AbstractOptParser
{
opt
[
File
](
'I'
,
"inputFile"
)
required
()
unbounded
()
valueName
"<vcf file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
inputFile
=
x
)
}
text
"Input
is a required file property
"
}
text
"Input
VCF file. Mandatory field
"
opt
[
File
](
'B'
,
"bedFile"
)
required
()
unbounded
()
valueName
"<bed file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
bedFile
=
x
)
}
text
"Bedfile
is a required file property
"
}
text
"
Input
Bed
file
. Mandatory field
"
opt
[
File
](
'o'
,
"output"
)
required
()
unbounded
()
valueName
"<vcf file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
outputFile
=
x
)
}
text
"
o
ut
is a required file property
"
}
text
"
O
ut
put VCF file. Mandatory field
"
opt
[
String
](
'f'
,
"fieldName"
)
required
()
unbounded
()
valueName
"<name of field in vcf file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
fieldName
=
x
)
}
text
"Name of info field in new vcf file"
opt
[
String
](
'd'
,
"fieldDescription"
)
unbounded
()
valueName
"<
name
of field in vcf file>"
action
{
(
x
,
c
)
=>
opt
[
String
](
'd'
,
"fieldDescription"
)
unbounded
()
valueName
"<
description
of field in vcf file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
fieldDescription
=
x
)
}
text
"Description of field in new vcf file"
opt
[
String
](
't'
,
"fieldType"
)
unbounded
()
valueName
"<
nam
e of field in vcf file>"
action
{
(
x
,
c
)
=>
opt
[
String
](
't'
,
"fieldType"
)
unbounded
()
valueName
"<
typ
e of field in vcf file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
fieldType
=
x
)
}
text
"
Description
of field in new vcf file"
}
text
"
Type
of field in new vcf file
. Can be 'Integer', 'Flag', 'Character', 'Float'
"
}
/**
...
...
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