Commit 0e0d9574 authored by Jerome Mariette's avatar Jerome Mariette
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parent ab5b8634
......@@ -20,12 +20,15 @@ from ng6.ng6workflow import NG6Workflow
class RNAdiversity (NG6Workflow):
def process(self):
# archive the files
addrawfiles = self.add_component("AddRawFiles", [self.runobj, self.args["input_files"], self.args["compression"]])
# clean reads and alignment
if self.args["input_files"].endswith('.sff'):
sff_pre_treatment = self.add_component("MothurShhhFlows", kwargs={'sff_files':self.args["input_files"],'sample_barcodes':self.args["sample_barcodes"]})
trim_fasta = self.add_component("MothurTrimSeqs", kwargs={'fasta_files':sff_pre_treatment.shhh_fasta_files,'names_files':sff_pre_treatment.names_files,\
'groups_files':sff_pre_treatment.groups_files,'forward_primer':self.args["forward_primer"],'reverse_primer':self.args["reverse_primer"],'sample_barcodes':self.args["sample_barcodes"]}\
,parent = sff_pre_treatment)
shhh_flows = self.add_component("MothurShhhFlows", kwargs={'sff_files':self.args["input_files"],'sample_barcodes':self.args["sample_barcodes"]})
trim_fasta = self.add_component("MothurTrimSeqs", kwargs={'fasta_files':shhh_flows.shhh_fasta_files,'names_files':shhh_flows.names_files,\
'groups_files':shhh_flows.groups_files,'forward_primer':self.args["forward_primer"],'reverse_primer':self.args["reverse_primer"],'sample_barcodes':self.args["sample_barcodes"]}\
,parent = shhh_flows)
elif self.args["input_files"].endswith('.fasta'):
trim_fasta = self.add_component("MothurTrimSeqs", kwargs={'fasta_files':self.args["input_files"],'forward_primer':self.args["forward_primer"],\
'reverse_primer':self.args["reverse_primer"]}, component_prefix="fasta")
......@@ -44,5 +47,6 @@ class RNAdiversity (NG6Workflow):
distseqs = self.add_component("MothurDistSeqs", [chimerauchime.pick_fasta_files])
cluster = self.add_component("MothurCluster", [distseqs.dist_files,chimerauchime.pick_names_files])
otuanalysis = self.add_component("MothurOTUAnalysis", kwargs={'an_list_files':cluster.an_list_files,'groups_files':chimerauchime.pick_groups_files,\
'names_files':chimerauchime.pick_names_files,'taxonomy_files':classifyseqs.taxonomy_files,'label':self.args["label"],'tree_label':self.args["label"]},parent=chimerauchime)
# pour l'analyse d'OTU peut etre mettre en place direct EspritTree
'names_files':chimerauchime.pick_names_files,'taxonomy_files':classifyseqs.taxonomy_files,'label':self.args["labels"],'tree_label':self.args["labels"]},parent=chimerauchime)
# TODO: add EspritTree and Usearch v7.0
......@@ -36,6 +36,12 @@ input_files.flag = --input-files
input_files.help = Where is the input file to process is stored (sff or fasta file)
input_files.required = True
compression.name = compression
compression.flag = --compression
compression.help = How should data be compressed once archived (none|gz|bz2)
compression.default = none
compression.choices = none|gz|bz2
reference_alignment.name = reference_alignment
reference_alignment.flag = --reference-alignment
reference_alignment.help = Where is stored the reference alignment
......@@ -54,10 +60,6 @@ sample_barcodes.name = sample_barcodes
sample_barcodes.flag = --sample-barcodes
sample_barcodes.help = Which barcodes were used in the experimentation : "sampleName1:barcodeString1;sampleName2:barcodeString2"
reference_chimera.name = reference_chimera
reference_chimera.flag = --reference-chimera
reference_chimera.help = which reference databank should be used to detect chimer
classify_template.name = classify_template
classify_template.flag = --classify-template
classify_template.help = Which template file should be used to classify reads
......@@ -68,7 +70,7 @@ classify_taxonomy.flag = --classify-taxonomy
classify_taxonomy.help = Which taxonomy file should be used to classify reads
classify_taxonomy.required = True
label.name = label
label.flag = --label
label.type = str
label.help = unique-0.03-0.05-0.10
\ No newline at end of file
labels.name = labels
labels.flag = --labels
labels.type = str
labels.help = unique-0.03-0.05-0.10
\ No newline at end of file
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