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Maintenance - Mise à jour mensuelle Lundi 6 Février entre 7h00 et 9h00
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genotoul-bioinfo
ng6
Commits
e0dd583d
Commit
e0dd583d
authored
Apr 24, 2013
by
Penom Nom
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parent
5b1ec377
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1
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workflows/r454_diversity/components/mothurmakeshared.py
View file @
e0dd583d
...
...
@@ -10,13 +10,17 @@ class MothurMakeShared(Component):
Create a table that indicates the number of times an OTU shows up in each sample
"""
def
define_parameters
(
self
,
an_list_files
,
groups_files
):
def
define_parameters
(
self
,
an_list_files
,
groups_files
,
label
=
"unique-0.01"
):
"""
:param an_list_files: an list files to process
:type an_list_files: str
:param groups_files: groups files to process
:type groups_files: str
:param label :
:type label : str
"""
#define parameters
self
.
label
=
label
#define input files
self
.
an_list_files
=
InputFileList
(
an_list_files
)
self
.
groups_files
=
InputFileList
(
groups_files
,
Formats
.
MOTHUR_GROUPS
)
...
...
@@ -25,5 +29,6 @@ class MothurMakeShared(Component):
self
.
stdout
=
OutputFileList
(
self
.
get_outputs
(
'{basename_woext}.stdout'
,
self
.
an_list_files
))
def
process
(
self
):
print
">>>Process make.shared"
makeshared
=
ShellFunction
(
self
.
get_exec_path
(
"mothur"
)
+
' "#make.shared(list=$1,group=$2,outputdir='
+
self
.
output_directory
+
'/)" > $3'
,
cmd_format
=
'{EXE} {IN} {OUT}'
)
makeshared
=
ShellFunction
(
self
.
get_exec_path
(
"mothur"
)
+
' "#make.shared(list=$1,group=$2,label='
+
self
.
label
+
',outputdir='
+
self
.
output_directory
+
'/)" > $3'
,
\
cmd_format
=
'{EXE} {IN} {OUT}'
)
makeshared
=
MultiMap
(
makeshared
,
inputs
=
[
self
.
an_list_files
,
self
.
groups_files
],
outputs
=
[
self
.
stdout
,
self
.
an_shared_files
])
\ No newline at end of file
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