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genotoul-bioinfo
ng6
Commits
4ed31b07
Commit
4ed31b07
authored
Apr 12, 2013
by
Jerome Mariette
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parent
cd66b796
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2
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workflows/r454_diversity/__init__.py
View file @
4ed31b07
...
...
@@ -42,17 +42,15 @@ class RNAdiversity (Workflow):
trimseqs
=
self
.
add_component
(
"MothurTrimSeqs"
,[
shhhflows
.
fasta_files
,
oligos_fullpath
,
shhhflows
.
names_files
])
uniqueseqs
=
self
.
add_component
(
"MothurUniqueSeqs"
,[
trimseqs
.
trim_fasta_files
,
trimseqs
.
trim_names_files
])
alignseqs
=
self
.
add_component
(
"MothurAlignSeqs"
,[
uniqueseqs
.
unique_fasta_files
,
self
.
args
[
"reference_alignment"
]])
summaryseqs_align
=
self
.
add_component
(
"MothurSummarySeqs"
,
[
alignseqs
.
align_files
,
uniqueseqs
.
unique_names_files
],
component_prefix
=
"align"
)
#screenseqs = self.add_component("MothurScreenSeqs",[alignseqs.align_files,uniqueseqs.names_files,trimseqs.groups_files])
#summaryseqs_screen = self.add_component("MothurSummarySeqs", [screenseqs.good_align_files,screenseqs.good_names_files],{},"screen")
#filterseqs = self.add_component("MothurFilterSeqs",[screenseqs.good_align_files])
#uniqueseqs_filter = self.add_component("MothurUniqueSeqs",[filterseqs.filter_fasta_files,screenseqs.good_names_files],{},"filter")
#precluster = self.add_component("MothurPreCluster",[uniqueseqs_filter.unique_fasta_files,uniqueseqs_filter.names_files,screenseqs.good_groups_files])
#summaryseqs_precluster = self.add_component("MothurSummarySeqs", [precluster.precluster_fasta_files,precluster.precluster_names_files],{},"precluster")
#chimerauchime = self.add_component("MothurChimeraUchime",[precluster.precluster_fasta_files,precluster.precluster_names_files,screenseqs.good_groups_files])
#removeseqs = self.add_component("MothurRemoveSeqs",[chimerauchime.uchime_accnos_files,precluster.precluster_fasta_files,precluster.precluster_names_files,\
# screenseqs.good_groups_files])
#summaryseqs_removeseqs = self.add_component("MothurSummarySeqs", [removeseqs.pick_fasta_files,removeseqs.pick_names_files],{},"removeseqs")
#classifyseqs = self.add_component("MothurClassifySeqs",[removeseqs.pick_fasta_files,removeseqs.pick_names_files,removeseqs.pick_groups_files,self.args["template"],\
# self.args["taxonomy"]])
# removegroups = self.add_component("MothurRemoveGroups", [removeseqs.pick_fasta_files,removeseqs.pick_names_files,removeseqs.pick_groups_files,classifyseqs.taxonomy_files])
...
...
workflows/r454_diversity/components/mothursummaryseqs.py
View file @
4ed31b07
...
...
@@ -27,7 +27,7 @@ class MothurSummarySeqs(Component):
if
names_files
:
self
.
names_files
=
InputFileList
(
self
.
names_files
,
Formats
.
MOTHUR_NAMES
)
#define output files
self
.
summary_files
=
OutputFileList
(
self
.
get_outputs
(
'{basename_woext}.summary'
,
self
.
fasta_files
)
,
Formats
.
MOTHUR_SUMMARY
)
self
.
summary_files
=
OutputFileList
(
self
.
get_outputs
(
'{basename_woext}.summary'
,
self
.
fasta_files
))
self
.
stdout
=
OutputFileList
(
self
.
get_outputs
(
'{basename_woext}.stdout'
,
self
.
fasta_files
))
def
process
(
self
):
...
...
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