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biopet.biopet
Commits
d44f4f5d
Commit
d44f4f5d
authored
Nov 21, 2016
by
Peter van 't Hof
Browse files
Added text to arguments
parent
91af94b8
Changes
1
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Inline
Side-by-side
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/DownloadNcbiAssembly.scala
View file @
d44f4f5d
...
@@ -21,22 +21,22 @@ object DownloadNcbiAssembly extends ToolCommand {
...
@@ -21,22 +21,22 @@ object DownloadNcbiAssembly extends ToolCommand {
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
{
opt
[
String
](
'a'
,
"assembly id"
)
required
()
unbounded
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
opt
[
String
](
'a'
,
"assembly id"
)
required
()
unbounded
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
assemblyId
=
x
)
c
.
copy
(
assemblyId
=
x
)
}
}
text
"refseq ID from NCBI"
opt
[
File
](
'o'
,
"output"
)
required
()
unbounded
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
opt
[
File
](
'o'
,
"output"
)
required
()
unbounded
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
outputFile
=
x
)
c
.
copy
(
outputFile
=
x
)
}
}
text
"output Fasta file"
opt
[
File
](
"report"
)
unbounded
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
opt
[
File
](
"report"
)
unbounded
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
reportFile
=
Some
(
x
))
c
.
copy
(
reportFile
=
Some
(
x
))
}
}
text
"where to write report from ncbi"
opt
[
String
](
"nameHeader"
)
unbounded
()
valueName
"<string>"
action
{
(
x
,
c
)
=>
opt
[
String
](
"nameHeader"
)
unbounded
()
valueName
"<string>"
action
{
(
x
,
c
)
=>
c
.
copy
(
contigNameHeader
=
Some
(
x
))
c
.
copy
(
contigNameHeader
=
Some
(
x
))
}
}
text
"What column to use from the NCBI report for the nam,e of the contigs"
opt
[(
String
,
String
)](
"mustHaveOne"
)
unbounded
()
valueName
"<
string
>"
action
{
(
x
,
c
)
=>
opt
[(
String
,
String
)](
"mustHaveOne"
)
unbounded
()
valueName
"<
column_name=regex
>"
action
{
(
x
,
c
)
=>
c
.
copy
(
mustHaveOne
=
(
x
.
_1
,
x
.
_2
)
::
c
.
mustHaveOne
)
c
.
copy
(
mustHaveOne
=
(
x
.
_1
,
x
.
_2
)
::
c
.
mustHaveOne
)
}
}
text
"This can be used to filter based on the NCBI report, multiple conditions can be given, at least 1 should be true"
opt
[(
String
,
String
)](
"mustNotHave"
)
unbounded
()
valueName
"<
string
>"
action
{
(
x
,
c
)
=>
opt
[(
String
,
String
)](
"mustNotHave"
)
unbounded
()
valueName
"<
column_name=regex
>"
action
{
(
x
,
c
)
=>
c
.
copy
(
mustNotHave
=
(
x
.
_1
,
x
.
_2
)
::
c
.
mustNotHave
)
c
.
copy
(
mustNotHave
=
(
x
.
_1
,
x
.
_2
)
::
c
.
mustNotHave
)
}
}
text
"This can be used to filter based on the NCBI report, multiple conditions can be given, all should be false"
}
}
/**
/**
...
...
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