Commit bfb70b03 authored by Penom Nom's avatar Penom Nom
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parent d3e732bb
......@@ -51,16 +51,17 @@ class RNAdiversity (Workflow):
else:
chimerauchime = self.add_component("MothurChimeraUchime",kwargs={'fasta_files':precluster.precluster_fasta_files,'names_files':precluster.precluster_names_files,\
'groups_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])
removeseqs = self.add_component("MothurRemoveSeqs",[chimerauchime.uchime_accnos_files,precluster.precluster_fasta_files,precluster.precluster_names_files,\
screenseqs.good_groups_files])
#Analysis MothurClassify
#classifyseqs = self.add_component("MothurClassifySeqs",[removeseqs.pick_fasta_files,self.args["template"],self.args["taxonomy"],removeseqs.pick_names_files,\
# removeseqs.pick_groups_files])
#krona_classifyseqs = self.add_component("MothurKrona", [classifyseqs.taxonomy_files,removeseqs.pick_names_files,removeseqs.pick_groups_files],{},"classifyseqs")
classifyseqs = self.add_component("MothurClassifySeqs",[removeseqs.pick_fasta_files,self.args["template"],self.args["taxonomy"],removeseqs.pick_names_files,\
removeseqs.pick_groups_files])
krona_classifyseqs = self.add_component("MothurKrona", [classifyseqs.taxonomy_files,removeseqs.pick_names_files,removeseqs.pick_groups_files],{},"classifyseqs")
# removegroups = self.add_component("MothurRemoveGroups", [removeseqs.pick_fasta_files,removeseqs.pick_names_files,removeseqs.pick_groups_files,chimerauchime.uchime_accnos_files])
#distseqs = self.add_component("MothurDistSeqs", [removeseqs.pick_fasta_files])
#cluster = self.add_component("MothurCluster", [distseqs.dist_files,removeseqs.pick_names_files])
#makeshared = self.add_component("MothurMakeShared", [cluster.an_list_files,removeseqs.pick_groups_files])
#venn = self.add_component("MothurVenn", [makeshared.an_shared_files])
#classifyotu = self.add_component("MothurClassifyOtu", [cluster.an_list_files,classifyseqs.taxonomy_files,removeseqs.pick_names_files,removeseqs.pick_groups_files])
#krona_classifyotu = self.add_component("MothurKrona", [classifyotu.cons_taxonomy_files],{},"classifyotu")
#Analysis OTUAnalysis
distseqs = self.add_component("MothurDistSeqs", [removeseqs.pick_fasta_files])
cluster = self.add_component("MothurCluster", [distseqs.dist_files,removeseqs.pick_names_files])
makeshared = self.add_component("MothurMakeShared", [cluster.an_list_files,removeseqs.pick_groups_files])
treeshared = self.add_component("MothurTreeShared", [makeshared.an_shared_files])
classifyotu = self.add_component("MothurClassifyOtu", [cluster.an_list_files,classifyseqs.taxonomy_files,removeseqs.pick_names_files,removeseqs.pick_groups_files])
krona_classifyotu = self.add_component("MothurKrona", [classifyotu.cons_taxonomy_files],{},"classifyotu")
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