def task_plot_MaAsLin_association():
return dodict([
"Rscript --vanilla d:utils/plot.R d:{OUTPUT}/MaAsLin_OUTPUT_OTU/OTU.txt",
"t:{OUTPUT}/MaAsLin_OUTPUT_OTU/OTU.pdf d:{OUTPUT}/MaAsLin_OUTPUT_MODULE/MODULE.txt",
"t:{OUTPUT}/MaAsLin_OUTPUT_MODULE/MODULE.pdf"
],
alias=alias)
def task_merge_otu_tables():
return dodict([
"merge_otu_tables.py -i",
"{OUTPUT}/AG_taxa/OTU_L2.biom,{OUTPUT}/AG_taxa/OTU_L3.biom,{OUTPUT}/AG_taxa/OTU_L4.biom,{OUTPUT}/AG_taxa/OTU_L5.biom,{OUTPUT}/AG_taxa/OTU_L6.biom",
"-o t:{OUTPUT}/summed_AG.biom"
],
clean=True,
alias=alias)
def task_plot_HAllA_Module_association():
return dodict([
"hallagram d:{OUTPUT}/HAllA_OUTPUT_Module/similarity_table.txt d:{OUTPUT}/HAllA_OUTPUT_Module/hypotheses_tree.txt",
"d:{OUTPUT}/HAllA_OUTPUT_Module/associations.txt",
"--cmap Reds --outfile t:{OUTPUT}/HAllA_OUTPUT_Module/hallagram_strongest_50.pdf --strongest 50",
"--similarity NMI --axlabels \"Metadata\" \"Metabolomic pathway modules\""
],
alias=alias)
def task_prepare_data_tables():
return dodict([
"Rscript --vanilla d:./utils/data_prep.R d:{INPUT}/{SAMPLE_IDS}",
"d:{OUTPUT}/summed_AG.txt d:{OUTPUT}/humann2_pathabundance_names.tsv",
"d:{INPUT}/{METADATA} t:{OUTPUT}/HAllA_INPUT/HAllA_Metadata.tsv",
"t:{OUTPUT}/HAllA_INPUT/HAllA_Module.tsv t:{OUTPUT}/HAllA_INPUT/HAllA_OTU.tsv",
"t:{OUTPUT}/MaAsLin_INPUT/MODULE.tsv t:{OUTPUT}/MaAsLin_INPUT/OTU.tsv"
],
alias=alias)
def task_convert_biom2tsv():
return dodict([
"biom convert -i d:{OUTPUT}/summed_AG.biom",
"-o t:{OUTPUT}/summed_AG.txt --table-type=\"OTU table\" --to-tsv"
],
alias=alias)
def task_summarize_taxa():
return dodict([
"summarize_taxa.py -i d:{OUTPUT}/OTU.biom -o T:{OUTPUT}/AG_taxa -L 2,3,4,5,6,7 "
],
clean=True,
alias=alias)
def task_filter_otus_from_otu_table():
return dodict([
"filter_otus_from_otu_table.py -i d:{INPUT}/{OTU_BIOM} ",
"-s 5 -n 3 -o t:{OUTPUT}/OTU.biom"
],
alias=alias)
def task_test_association_HAllA_MODULE():
return dodict([
"halla -X d:{OUTPUT}/HAllA_INPUT/HAllA_Metadata.tsv -Y d:{OUTPUT}/HAllA_INPUT/HAllA_Module.tsv",
"-o t:{OUTPUT}/HAllA_OUTPUT_Module -q .05", " --header"
],
alias=alias)
def task_test_association_MAASLIN_OTU():
return dodict([
"sh d:utils/test_associations.sh d:{OUTPUT}/MaAsLin_INPUT/OTU.tsv",
"d:{INPUT}/maaslin_config/maaslin_config_otu.txt t:{OUTPUT}/MaAsLin_OUTPUT_OTU/OTU.txt"
],
alias=alias)
def task_test_association_MAASLIN_MODULE():
return dodict([
"sh d:utils/test_associations.sh d:{OUTPUT}/MaAsLin_INPUT/MODULE.tsv",
"d:{INPUT}/maaslin_config/maaslin_config_module.txt t:{OUTPUT}/MaAsLin_OUTPUT_MODULE/MODULE.txt"
],
alias=alias)
