Mercurial > repos > iuc > picrust2_metagenome_pipeline
changeset 0:415cb5d91168 draft default tip
planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sat Mar 04 20:27:42 2023 +0000 @@ -0,0 +1,344 @@ +<?xml version="1.0"?> +<macros> + <token name="@TOOL_VERSION@">2.5.1</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">22.01</token> + <xml name="bio_tool"> + <xrefs> + <xref type="bio.tools">picrust2</xref> + </xrefs> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">picrust2</requirement> + <yield/> + </requirements> + </xml> + <token name="@HELP_HEADER@"> +What it does +============ + +PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of +Unobserved States) is a tool for predicting functional abundances based only on +marker gene sequences. + +Read more about the tool: https://github.com/picrust/picrust2/wiki + </token> + <xml name="citations"> + <citations> + <citation type="doi">10.1038/s41587-020-0548-6</citation> + </citations> + </xml> + + + + <token name="@VAR_ACCESS_FOO@"><![CDATA[ + ## in picrust2_pipeline the parameters are within a section or a + ## conditional. in the separate sections they are not. + ## this function allows unified access + #def getVarCond($sec_cond, $var) + #if $varExists($var) + #return $getVar($var) + #else if $varExists($sec_cond + "." + $var) + #return $getVar($sec_cond + "." + $var) + #else + #return + #end if + #end def + ]]></token> + + <!-- macros for place_seqs --> + + <token name="@PLACE_SEQS_PREPROCESSING@"><![CDATA[ + ## determine project dir which is something like /lib/python3.8/site-packages/picrust2/default_files/ + PROJECT_DIR=\$(python -c 'from picrust2 import default; print(default.project_dir)') && + REF_DIR_BASE=\$PROJECT_DIR"/default_files/" && + #if $getVarCond("place_seqs_section", "ref_dir.selector") == "custom" + mkdir -p custom/ && + ln -s '$getVarCond("place_seqs_section", "ref_dir.custom_fna")' custom/custom.fna && + ln -s '$getVarCond("place_seqs_section", "ref_dir.custom_hmm")' custom/custom.hmm && + #if $getVarCond("place_seqs_section", "placement_tool") == "epa-ng" + ln -s '$getVarCond("place_seqs_section", "ref_dir.custom_model")' custom/custom.model && + #else if $getVarCond("place_seqs_section", "placement_tool") + ln -s '$getVarCond("place_seqs_section", "ref_dir.custom_model")' custom/custom.raxml_info && + #end if + ln -s '$getVarCond("place_seqs_section", "ref_dir.custom_tre")' custom/custom.tre && + #end if + ]]></token> + <token name="@PLACE_SEQS_PARAMS@"><![CDATA[ + --study_fasta '$getVarCond("place_seqs_section", "study_fasta")' + --placement_tool '$getVarCond("place_seqs_section", "placement_tool")' + ## set refdir (default is prokaryotic), even if the default will + ## be treated internally as `"\$REF_DIR_BASE"$ref_dir.selector` + ## picrust2 will complain about non-default reference files + ## specified with default pathway mapfile + #if $getVarCond("place_seqs_section", "ref_dir.selector") == "custom" + --ref_dir custom/ + #else if $getVarCond("place_seqs_section", "ref_dir.selector") != "prokaryotic/pro_ref/" + --ref_dir "\$REF_DIR_BASE"$getVarCond("place_seqs_section", "ref_dir.selector") + #end if + --min_align $getVarCond("place_seqs_section", "min_align") + ]]></token> + <xml name="place_seqs_params"> + <param argument="--study_fasta" type="data" format="fasta" label="Study sequences" help="Sequences of the representative OTUs and/or ASVs. Sequences need to be on the positive strand and the headerline should be only one field, i.e. no additional whitespace-delimited fields"/> + <param argument="--placement_tool" type="select" label="Placement tool" help="Used for placing sequences into reference tree"> + <option value="epa-ng" selected="true">EPA-ng - Fast, parallel, highly accurate Maximum Likelihood Phylogenetic Placement, by the team behind RAxML(-ng)</option> + <option value="sepp">SEPP - SATe-enabled Phylogenetic Placement</option> + </param> + <conditional name="ref_dir"> + <param name="selector" type="select" label="Reference data" help="Used for sequence placement"> + <option value="prokaryotic/pro_ref/" selected="true">Prokaryotic 16S rRNA gene</option> + <!-- TODO https://github.com/picrust/picrust2/issues/276 --> + <option value="fungi/fungi_ITS/">Fungal ITS (only for epa-ng)</option> + <option value="fungi/fungi_18S/">Fungal 18S (only for epa-ng)</option> + <option value="custom">Custom reference sequence files</option> + </param> + <when value="prokaryotic/pro_ref/"/> + <when value="fungi/fungi_ITS/"/> + <when value="fungi/fungi_18S/"/> + <when value="custom"> + <param name="custom_fna" type="data" format="fasta" label="Multiple-sequence alignment of reference sequences"/> + <param name="custom_hmm" type="data" format="hmm2,hmm3" label="Hidden-markov model of the multiple-sequence alignment" help="The HMM of the alignment can be created using hmmbuild"/> + <param name="custom_tre" type="data" format="newick" label="Tree of the reference sequences"/> + <param name="custom_model" type="data" format="txt" label="Modelfile" help="For epa-ng: output by RaXmL specifying the best parameters for the tree, for sepp see examples in PICRUSt2 repository"/> + </when> + </conditional> + <param argument="--min_align" type="float" value="0.80" min="0.0" max="1.0" label="Minimum alignment length" help="Proportion of the total length of an input query sequence that must align with reference sequences. Sequences with lengths below this value will be excluded from the placement and all subsequent steps"/> + </xml> + <xml name="place_seqs_output" tokens="from_work_dir" token_label_suffix=""> + <data name="out_tree" format="newick" from_work_dir="@FROM_WORK_DIR@/out.tre" label="${tool.name} on ${on_string}: Tree of reference and study 16S sequences @LABEL_SUFFIX@"/> + <collection name="place_seqs_intermediate_output" type="list" label="${tool.name} on ${on_string}: Intermediate files @LABEL_SUFFIX@" > + <discover_datasets pattern="__name_and_ext__" directory="@FROM_WORK_DIR@/intermediate/place_seqs/"/> + <yield/> + </collection> + </xml> + + <!-- parameters of hsp --> + <token name="@HSP_PARAMS@"><![CDATA[ + ## hsp and picrust2_pipeline + #if $getVarCond("hsp_section", "trait_input.selector") == "default" + #if $varExists('trait_input.in_trait') + --in_trait '$trait_input.in_trait' + #else if $varExists('hsp_section.trait_input.in_traits') + --in_traits '$hsp_section.trait_input.in_traits' + #else + #raise Exception("wrapper must define in_trait / in_traits") + #end if + #else if $getVarCond("hsp_section", "trait_input.selector") == "custom" + #if $varExists('trait_input.observed_trait_table') + --observed_trait_table '$trait_input.observed_trait_table' + #else if $varExists('hsp_section.trait_input.custom_trait_tables') + --custom_trait_tables '$hsp_section.trait_input.custom_trait_tables' + --marker_gene_table '$hsp_section.trait_input.marker_gene_table' + #else + #raise Exception("wrapper must define observed_trait_table / (custom_trait_tables + marker_gene_table)") + #end if + #end if + + + --hsp_method '$getVarCond("hsp_section", "hsp_method_options.hsp_method")' + #if $getVarCond("hsp_section", "hsp_method_options.hsp_method") == "mp" + --edge_exponent $getVarCond("hsp_section", "hsp_method_options.edge_exponent") + #else if $getVarCond("hsp_section", "") == "emp_prob" + ## special treatment of seed (option absent in picrust2_pipeline) + #if $varExists('hsp_method_options') and has_attrib($hsp_method_options, "seed") + --seed $hsp_method_options.seed + #end if + #end if + ## hsp and picrust2_pipeline use different CLI params to toggle NSTI computation + #if $varExists('calculate_NSTI') + $calculate_NSTI + #else if $varExists('hsp_section.skip_nsti') + $hsp_section.skip_nsti + #else + #raise Exception("wrapper must define calculate_NSTI / skip_nsti") + #end if + ]]></token> + <!-- - one of nsti_[true,false]value must be given: CLI param + differs between hsp and picrust2_pipeline + - nsti_checked must be set accordingly to true or false + + furthermore there three yields can be used (2 names & 1 unnamed) + - the unnamed is used to add the seed param for hsp (for \-\-hsp_method emp_prob) + - the named yield `add_default_traits` is used to add two default trait tables for hsp + - the named yield `custom_traits` is used for the different parameters + to specify custom trait tables in hsp (observed_trait_table) and + picrust2_pipeline (custom_trait_tables, marker_gene_table) + --> + <xml name="hsp_params" tokens="nsti_checked,in_trait_arg,in_trait_multiple,in_trait_label_suff" token_nsti_truevalue="" token_nsti_falsevalue="" token_in_traits_help=""> + <conditional name="trait_input"> + <param name="selector" type="select" label="Trait table@IN_TRAIT_LABEL_SUFF@" help="i.e. which gene families to predict"> + <option value="default" selected="true">Default trait table@IN_TRAIT_LABEL_SUFF@</option> + <option value="custom">Customized trait table@IN_TRAIT_LABEL_SUFF@</option> + </param> + <when value="default"> + <param argument="@IN_TRAIT_ARG@" type="select" multiple="@IN_TRAIT_MULTIPLE@" optional="false" label="Pre-calculated trait table@IN_TRAIT_LABEL_SUFF@" help="@IN_TRAITS_HELP@"> + <option value="COG">Clusters of Orthologous Genes database (COG)</option> + <option value="EC" selected="true">Enzyme Commission number database (EC number)</option> + <option value="KO" selected="true">KEGG Orthology database (KO)</option> + <option value="PFAM">Pfam database</option> + <option value="TIGRFAM">TIGRFAM database</option> + <yield name="add_default_traits"/> + </param> + </when> + <when value="custom"> + <yield name="custom_traits"/> + </when> + </conditional> + <conditional name="hsp_method_options"> + <param argument="--hsp_method" type="select" label="Hidden-state prediction method"> + <option value="mp" selected="true">Predict discrete traits by: Maximum parsimony (mp)</option> + <option value="emp_prob">Predict discrete traits by: Empirical state probabilities across tips (emp_prob)</option> + <option value="subtree_average">Predict continuous traits by: Subtree averaging (subtree_average)</option> + <option value="pic">Predict continuous traits by: phylogentic independent contrast (pic)</option> + <option value="scp">Reconstruct continuous traits by: squared-change parsimony (scp)</option> + </param> + <when value="mp"> + <param argument="--edge_exponent" type="float" value="0.5" min="0.0" label="Transition cost weight" help="Specifies weighting transition costs by the inverse length of edge lengths. If 0, then edge lengths do not influence predictions"/> + </when> + <when value="emp_prob"> + <yield/> + </when> + <when value="subtree_average"/> + <when value="pic"/> + <when value="scp"/> + </conditional> + <param argument="@NSTI_TRUEVALUE@@NSTI_FALSEVALUE@" type="boolean" truevalue="@NSTI_TRUEVALUE@" falsevalue="@NSTI_FALSEVALUE@" checked="@NSTI_CHECKED@" label="Calculate NSTI and add to output file" help="And add to output file"/> + </xml> + + <!-- parameters of the metagenome_pipeline --> + + <token name="@PREPARE_METAGENOME_PIPELINE_PARAMS@"><![CDATA[ +#set $_input=$getVarCond("metagenome_pipeline_section", "input") +#if $_input.ext == "mothur.shared" + #set ext="msf" +#else if $_input.ext == "tabular" + #set ext="tsv" +#else if $_input.ext.startswith('biom') + #set ext="biom" +#else + >&2 "unknown extension $_input.ext" + exit 1; +#end if +ln -s '$input' 'input.$ext' && + ]]></token> + <token name="@METAGENOME_PIPELINE_PARAMS@"><![CDATA[ +--input 'input.$ext' +#if $getVarCond("metagenome_pipeline_section", "input_options.selector") == "ASV" + --min_reads $getVarCond("metagenome_pipeline_section", "input_options.min_reads") + --min_samples $getVarCond("metagenome_pipeline_section", "input_options.min_samples") +#end if +$getVarCond("metagenome_pipeline_section", "stratified_output.selector") +#if $getVarCond("metagenome_pipeline_section", "stratified_output.selector") != '' + $getVarCond("metagenome_pipeline_section", "stratified_output.wide_table") +#end if +$getVarCond("metagenome_pipeline_section", "skip_norm") +--max_nsti $getVarCond("metagenome_pipeline_section", "max_nsti") + ]]></token> + <xml name="metagenome_pipeline_params" tokens="stratified_arg"> + <param argument="--input" type="data" format="tabular,biom1,biom2,mothur.shared" label="Sequence abundance table (OTUs or ASVs)" help="The sequence abundances should be in read counts and not relative abundances. The tool will normalize the input sequence abundance table by the predicted number of marker genes"/> + <conditional name="input_options"> + <param name="selector" type="select" label="Sequence abundance table type"> + <option value="OTU" selected="true">Operational Taxonomic Units (OTU)</option> + <option value="ASV">Amplicon Sequence Variants (ASV)</option> + </param> + <when value="OTU"> + </when> + <when value="ASV"> + <param argument="--min_reads" type="integer" min="1" value="1" label="Minimum number of reads across all samples for each input ASV" help="ASVs below this cut-off will be counted as part of the RARE category in the stratified output"/> + <param argument="--min_samples" type="integer" min="1" value="1" label="Minimum number of samples that an ASV needs to be identfied within" help="ASVs below this cut-off will be counted as part of the RARE category in the stratified output"/> + </when> + </conditional> + <yield/> + <param argument="--max_nsti" type="float" min="0" value="2.0" label="Maximum Nearest-sequenced taxon index (NSTI)" help="Sequences with larger values will be excluded"/> + <conditional name="stratified_output"> + <param argument="@STRATIFIED_ARG@" name="selector" type="select" label="Generate an output table stratified by sequences"> + <option value="" selected="true">No</option> + <option value="@STRATIFIED_ARG@">Yes [will increase run-time]</option> + </param> + <when value=""/> + <when value="@STRATIFIED_ARG@"> + <param argument="--wide_table" type="boolean" truevalue="--wide_table" falsevalue="" checked="false" label="Output wide-format stratified table of metagenome predictions" help="This is the deprecated method of generating stratified tables since it is extremely memory intensive"/> + </when> + </conditional> + <param argument="--skip_norm" type="boolean" truevalue="--skip_norm" falsevalue="" checked="false" label="Skip normalizing sequence abundances by predicted marker gene copy numbers"/> + </xml> + + <!-- pathway_pipeline macros--> + <token name="@PATHWAY_PIPELINE_PARAMS@"><![CDATA[ +## in pathway_pipeline its --map while in picrust2_pipeline its --pathway_map +#if $varExists('map') and $map + --map '$map' +#else if $varExists('predict_pathways.pathway_map') and $predict_pathways.pathway_map + --pathway_map '$predict_pathways.pathway_map' +#end if +$getVarCond("predict_pathways", "skip_minpath") +$getVarCond("predict_pathways", "no_gap_fill") +$getVarCond("predict_pathways", "regrouping.no_regroup") +#if $getVarCond("predict_pathways", "regrouping.no_regroup") == '' and $getVarCond("predict_pathways", "regrouping.regroup_map") + --regroup_map '$getVarCond("predict_pathways", "regroup_map")' +#end if +$getVarCond("predict_pathways", "strat_output.per_sequence_contrib") +#if $getVarCond("predict_pathways", "strat_output.per_sequence_contrib") != "" + --per_sequence_function '$getVarCond("predict_pathways", "strat_output.per_sequence_function")' + --per_sequence_abun '$getVarCond("predict_pathways", "strat_output.per_sequence_abun")' + $getVarCond("predict_pathways", "strat_output.wide_table") +#end if +$getVarCond("predict_pathways", "coverage") + ]]></token> + <xml name="pathway_pipeline_params" tokens="mapargument"> + <param argument="@MAPARGUMENT@" type="data" format="txt,tabular" optional="true" label="Customized table mapping of pathways to reactions" help="Default mapping file is Maps MetaCyc reactions to prokaryotic MetaCyc pathways"/> + <param argument="--skip_minpath" type="boolean" truevalue="" falsevalue="--skip_minpath" checked="true" label="Run MinPath to identify which pathways are present as a first pass"/> + <param argument="--no_gap_fill" type="boolean" truevalue="" falsevalue="--no_gap_fill" checked="true" label="Perform gap filling before predicting pathway abundances"/> + <conditional name="regrouping"> + <param argument="--no_regroup" type="select" label="Regroup input gene families to reactions"> + <option value="">Yes</option> + <option value="--no_regroup">No</option> + </param> + <when value=""> + <param argument="--regroup_map" type="data" format="tabular" optional="true" label="Mapfile of ids to regroup gene families to before running MinPath" help="Keep empty to use the default mapping file (ec_level4_to_metacyc_rxn.tsv contained in PICRUSt2)"/> + </when> + <when value="--no_regroup"/> + </conditional> + <conditional name="strat_output"> + <param argument="--per_sequence_contrib" type="select" label="Calculate pathway abundances for each individual predicted genome" help="The output will be the predicted pathway abundance contributed by each individual sequence. This is in contrast to the default stratified output, which is the contribution to the community-wide pathway abundances. Note this will greatly increase the runtime. Experimental pathway coverage stratified by contributing sequence will also be output when --coverage is set"> + <option value="--per_sequence_contrib">Yes</option> + <option value="" selected="true">No</option> + </param> + <when value="--per_sequence_contrib"> + <param argument="--per_sequence_abun" type="data" format="tabular" label="Table of sequence abundances across samples normalized by marker copy number" help="Typically the normalized sequence abundance table output at the metagenome pipeline step. This input is required when the per sequence contrib option is set"/> + <param argument="--per_sequence_function" type="data" format="tabular" label="Table of function abundances per sequence, which was outputted at the hidden-state prediction step" help="This input is required when the per sequence contrib option is set. Note that this file should be the same input table as used for the metagenome pipeline step"/> + <!-- TODO maybe deprecate .. because complicated anyway as its used in metagenome_pipeline as well and help says deprecated as well --> + <param argument="--wide_table" type="boolean" truevalue="--wide_table" falsevalue="" checked="false" label="Output wide-format stratified table (DEPRECATED)" help="Instead of the metagenome contribution table. This is the deprecated method of generating + stratified tables since it is extremely memory intensive"/> + </when> + <when value=""/> + </conditional> + <param argument="--coverage" type="boolean" truevalue="--coverage" falsevalue="" checked="false" label="Calculate pathway coverages as well as abundances" help="Experimental and only useful for advanced users"/> + </xml> + <xml name="pathways_output" tokens="from_work_dir" token_label_suffix=""> + <data name="pathways_output" format="tabular" from_work_dir="@FROM_WORK_DIR@/pathways_out/path_abun_unstrat.tabular" label="${tool.name} on ${on_string}: Pathway abundances"> + <yield/> + </data> + <collection name="pathways_intermediate_output" type="list" label="${tool.name} on ${on_string}: Intermediate files @LABEL_SUFFIX@" > + <discover_datasets pattern="__name_and_ext__" directory="@FROM_WORK_DIR@/intermediate/pathways/" format="tabular"/> + <yield name="intermediate_filter"/> + </collection> + <data format="tabular" name="path_cov_unstrat" from_work_dir="@FROM_WORK_DIR@/pathways_out/path_cov_unstrat.tabular" label="${tool.name} on ${on_string}: Pathway coverage @LABEL_SUFFIX@" > + <yield/> + <yield name="coverage_filter"/> + </data> + <data format="tabular" name="path_abun_unstrat_per_seq" from_work_dir="@FROM_WORK_DIR@/pathways_out/path_abun_unstrat_per_seq.tabular" label="${tool.name} on ${on_string}: Pathway abundance unstratified per sequence @LABEL_SUFFIX@" > + <yield/> + <yield name="per_sequence_filter"/> + </data> + <data format="tabular" name="path_abun_predictions" from_work_dir="@FROM_WORK_DIR@/pathways_out/path_abun_predictions.tabular" label="${tool.name} on ${on_string}: Pathway abundance predictions @LABEL_SUFFIX@" > + <yield/> + <yield name="per_sequence_filter"/> + </data> + <data format="tabular" name="path_abun_contrib" from_work_dir="@FROM_WORK_DIR@/pathways_out/path_abun_contrib.tabular" label="${tool.name} on ${on_string}: Pathway abundance contributed @LABEL_SUFFIX@" > + <yield/> + <yield name="per_sequence_filter"/> + </data> + </xml> +</macros> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/metagenome_pipeline.xml Sat Mar 04 20:27:42 2023 +0000 @@ -0,0 +1,213 @@ +<tool id="picrust2_metagenome_pipeline" name="PICRUSt2 Metagenome prediction" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>to generate per-sample metagenome functional profiles based on the predicted functions for each study sequence</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="bio_tool"/> + <expand macro="requirements"/> + <version_command>metagenome_pipeline.py -v</version_command> + <command detect_errors="exit_code"><![CDATA[ +@VAR_ACCESS_FOO@ +@PREPARE_METAGENOME_PIPELINE_PARAMS@ +metagenome_pipeline.py + --function '$function' + --marker '$marker' + @METAGENOME_PIPELINE_PARAMS@ + --out_dir 'metagenome_output' +&& find metagenome_output -name "*.gz" -exec gunzip {} \; +&& true + ]]></command> + <inputs> + <expand macro="metagenome_pipeline_params" stratified_arg="--strat_out"> + <param argument="--function" type="data" format="tabular" label="Table with predicted gene family copy numbers" help="This table is generated by the tool for Hidden state prediction (HSP)"/> + <param argument="--marker" type="data" format="tabular" label="Table of predicted marker gene (16S or other) copy numbers" help="This table is generated by the tool for Hidden state prediction (HSP)"/> + </expand> + </inputs> + <outputs> + <data name="pred_metagenome_unstrat" format="tabular" from_work_dir="metagenome_output/pred_metagenome_unstrat.tsv" label="${tool.name} on ${on_string}: Predicted per-sample metagenome functional profiles"/> + <data name="seqtab_norm" format="tabular" from_work_dir="metagenome_output/seqtab_norm.tsv" label="${tool.name} on ${on_string}: Normalized sequence abundance table"/> + <data name="weighted_nsti" format="tabular" from_work_dir="metagenome_output/weighted_nsti.tsv" label="${tool.name} on ${on_string}: Weighted nearest-sequenced taxon index (NSTI) values per-sample"/> + <data name="strat_output" format="tabular" from_work_dir="metagenome_output/pred_metagenome_contrib.tsv" label="${tool.name} on ${on_string}: Predicted per-sample metagenome functional profiles, stratified by sequence ids (i.e. taxonomic contributors)" > + <filter>stratified_output['selector'] != '' and not stratified_output['wide_table']</filter> + </data> + <data name="wide_table_output" format="tabular" from_work_dir="metagenome_output/pred_metagenome_strat.tsv" label="${tool.name} on ${on_string}: Predicted per-sample metagenome functional profiles, wide-format stratified by sequence ids (i.e. taxonomic contributors)" > + <filter>stratified_output['selector'] != '' and stratified_output['wide_table']</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="3"> + <param name="input" ftype="mothur.shared" value="table.mothur.shared"/> + <param name="function" ftype="tabular" value="EC_predicted.tsv.gz"/> + <param name="marker" ftype="tabular" value="16S_predicted_and_nsti.tsv.gz"/> + <param name="max_nsti" value="2.0"/> + <param name="skip_norm" value="false"/> + <conditional name="stratified_output"> + <param name="selector" value=""/> + </conditional> + <conditional name="input_options"> + <param name="selector" value="OTU"/> + </conditional> + <output name="pred_metagenome_unstrat" ftype="tabular"> + <assert_contents> + <has_text text="function"/> + <has_n_lines n="1000"/> + </assert_contents> + </output> + <output name="seqtab_norm" ftype="tabular"> + <assert_contents> + <has_text text="normalized"/> + <has_n_lines n="38"/> + </assert_contents> + </output> + <output name="weighted_nsti" ftype="tabular"> + <assert_contents> + <has_text text="weighted_NSTI"/> + <has_n_lines n="25"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="3"> + <param name="input" ftype="biom1" value="table.biom"/> + <param name="function" ftype="tabular" value="EC_predicted.tsv.gz"/> + <param name="marker" ftype="tabular" value="16S_predicted_and_nsti.tsv.gz"/> + <param name="max_nsti" value="2.0"/> + <param name="skip_norm" value="false"/> + <conditional name="stratified_output"> + <param name="selector" value=""/> + </conditional> + <conditional name="input_options"> + <param name="selector" value="ASV"/> + <param name="min_reads" value="1"/> + <param name="min_samples" value="1"/> + </conditional> + <output name="pred_metagenome_unstrat" ftype="tabular"> + <assert_contents> + <has_text text="function"/> + <has_n_lines n="1000"/> + </assert_contents> + </output> + <output name="seqtab_norm" ftype="tabular"> + <assert_contents> + <has_text text="normalized"/> + <has_n_lines n="38"/> + </assert_contents> + </output> + <output name="weighted_nsti" ftype="tabular"> + <assert_contents> + <has_text text="weighted_NSTI"/> + <has_n_lines n="25"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="4"> + <param name="input" ftype="biom1" value="table.biom"/> + <param name="function" ftype="tabular" value="EC_predicted.tsv.gz"/> + <param name="marker" ftype="tabular" value="16S_predicted_and_nsti.tsv.gz"/> + <param name="max_nsti" value="2.0"/> + <param name="skip_norm" value="false"/> + <conditional name="stratified_output"> + <param name="selector" value="--strat_out"/> + <param name="wide_table" value="true"/> + </conditional> + <conditional name="input_options"> + <param name="selector" value="ASV"/> + <param name="min_reads" value="1"/> + <param name="min_samples" value="1"/> + </conditional> + <output name="pred_metagenome_unstrat" ftype="tabular"> + <assert_contents> + <has_text text="function"/> + <has_n_lines n="1000"/> + </assert_contents> + </output> + <output name="seqtab_norm" ftype="tabular"> + <assert_contents> + <has_text text="normalized"/> + <has_n_lines n="38"/> + </assert_contents> + </output> + <output name="weighted_nsti" ftype="tabular"> + <assert_contents> + <has_text text="weighted_NSTI"/> + <has_n_lines n="25"/> + </assert_contents> + </output> + <output name="wide_table_output" ftype="tabular"> + <assert_contents> + <has_text text="EC:1.1.1.1"/> + <has_n_lines n="18101"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="4"> + <param name="input" ftype="biom1" value="table.biom"/> + <param name="function" ftype="tabular" value="EC_predicted.tsv.gz"/> + <param name="marker" ftype="tabular" value="16S_predicted_and_nsti.tsv.gz"/> + <param name="max_nsti" value="2.0"/> + <param name="skip_norm" value="false"/> + <conditional name="stratified_output"> + <param name="selector" value="--strat_out"/> + <param name="wide_table" value="false"/> + </conditional> + <conditional name="input_options"> + <param name="selector" value="ASV"/> + <param name="min_reads" value="1"/> + <param name="min_samples" value="1"/> + </conditional> + <output name="pred_metagenome_unstrat" ftype="tabular"> + <assert_contents> + <has_text text="function"/> + <has_n_lines n="1000"/> + </assert_contents> + </output> + <output name="seqtab_norm" ftype="tabular"> + <assert_contents> + <has_text text="normalized"/> + <has_n_lines n="38"/> + </assert_contents> + </output> + <output name="weighted_nsti" ftype="tabular"> + <assert_contents> + <has_text text="weighted_NSTI"/> + <has_n_lines n="25"/> + </assert_contents> + </output> + <output name="strat_output" ftype="tabular"> + <assert_contents> + <has_text text="100CHE6KO"/> + <has_n_lines n="298016"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +@HELP_HEADER@ + +Metagenome Pipeline +=================== +Reads in a sequence abundance table (the abundances of OTUs or ASVs in BIOM, TSV, or mothur shared file format), the predicted marker gene abundances, and the predicted gene family abundances (these last two files are output by hsp.py). + +Note +==== +Per-sample metagenome functional profiles are generated based on the predicted functions for each study sequence. Note that typically these sequences correspond to OTUs or ASVs. The specified sequence abundance table will be normalized by the predicted number of marker gene copies before outputting the final files by default. The sample metagenome table stratified by contributing ASVs can optionally also be output. + +The sequence abundances should be in read counts and not relative abundances. It will normalize the input sequence abundance table by the predicted number of marker genes. It will then determine the predicted functional profiles per sample. Output stratified by sequence ids (i.e. taxonomic contributors) will also be output if the --strat_out option is used. Also, rare ASVs can be collapsed into the same category in the stratified output table based on the --min_reads and --min_samples options. Note the output files are tab-delimited even if the input files was in BIOM format. The normalized sequence abundance table and the weighted nearest-sequenced taxon index values per-sample will also be output to the output directory as separate files. + +Input +===== +Table of sequence abundances (BIOM, TSV, or mothur shared file format). + +Output +====== +Metagenome predictions: + 1. Predicted per-sample metagenome functional profiles + 2. Normalized sequence abundance table + 3. Weighted nearest-sequenced taxon index (NSTI) values per-sample + 4. When chosen within the tool's parameters: Predicted per-sample metagenome functional profiles, stratified by sequence ids (i.e. taxonomic contributors) + 5. When chosen within the tool's parameters: Predicted per-sample metagenome functional profiles, wide-format stratified by sequence ids (i.e. taxonomic contributors) + + ]]></help> + <citations> + <citation type="doi">10.1038/s41587-020-0548-6</citation> + </citations> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/img_centroid_16S_aligned_head30.hmm Sat Mar 04 20:27:42 2023 +0000 @@ -0,0 +1,3680 @@ +HMMER3/f [3.1b2 | February 2015] +NAME img_centroid_16S_aligned_head30 +LENG 1219 +MAXL 1483 +ALPH DNA +RF no +MM no +CONS yes +CS no +MAP yes +DATE Wed Oct 10 17:19:17 2018 +NSEQ 15 +EFFN 1.680908 +CKSUM 4036506208 +STATS LOCAL MSV -13.3981 0.69577 +STATS LOCAL VITERBI -14.9113 0.69577 +STATS LOCAL FORWARD -6.1644 0.69577 +HMM A C G T + m->m m->i m->d i->m i->i d->m d->d + COMPO 1.37152 1.48531 1.23220 1.47755 + 1.26208 1.34388 1.26814 1.74440 + 0.30721 1.43238 3.65865 3.23874 0.04000 0.00000 * + 1 0.35395 2.43840 2.24483 2.25526 43 a - - - + 1.38629 1.38629 1.38629 1.38629 + 0.14543 3.65865 2.21110 1.46634 0.26236 1.09861 0.40547 + 2 2.12949 2.47053 0.36672 2.26761 44 g - - - + 1.38629 1.38629 1.38629 1.38629 + 0.05789 3.57112 3.57112 1.46634 0.26236 1.83302 0.17427 + 3 1.87475 1.35652 1.96136 0.80211 45 t - - - + 1.38629 1.38629 1.38629 1.38629 + 0.05789 3.57112 3.57112 1.46634 0.26236 1.83302 0.17427 + 4 1.83494 2.02013 0.70400 1.54583 46 g - 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/img_centroid_16S_aligned_head30.model Sat Mar 04 20:27:42 2023 +0000 @@ -0,0 +1,1 @@ +GTR{1.00319/2.79077/1.5301/0.87441/3.83966/1}+FU{0.229585/0.22008/0.298596/0.251739}+G4m{0.453141}, noname = 1-1582
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/img_centroid_16S_aligned_head30.tre Sat Mar 04 20:27:42 2023 +0000 @@ -0,0 +1,1 @@ +(2511231175_test:0.00417761132822863299,(2545824660_test:0.00000100000050002909,((2519899794_test:0.01391402030675637121,2511231166_test:0.00665538545236680611):0.06273674610653526273,(2511231070_test:0.19422053808301012467,((2513237222_test:0.12148702101162445199,((2511231199_test:0.00850377323667460445,((2511231131_test:0.00170862468873008008,2519899561_test:0.00086957288189634858):0.00880326207108816233,(2511231164_test:0.00085719433669428577,2531839192_test:0.00000100000050002909):0.00346417887233879630):0.00395490298225046298):0.08865976442951280234,(2511231155_test:0.07140328680188372246,2501846300_test:0.05302326674590653044):0.00922416804481126715):0.01707145563721565798):0.06770060455925869247,2516143006_test:0.22117635610892677489):0.02999032625748145400):0.06716203994881037032):0.09307592027052699613):0.00082512996392334335,2511231196_test:0.00000100000050002909):0.0;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/metadata.tsv Sat Mar 04 20:27:42 2023 +0000 @@ -0,0 +1,25 @@ +SampleID Facility Genotype +100CHE6KO PaloAlto KO +101CHE6WT PaloAlto WT +102CHE6WT PaloAlto WT +103CHE6KO PaloAlto KO +104CHE6KO PaloAlto KO +20CMK6KO Dalhousie KO +21CMK6WT Dalhousie WT +22CMK6KO Dalhousie KO +23CMK6WT Dalhousie WT +24CMK6KO Dalhousie KO +26CMK6WT Dalhousie WT +30CMK6KO Dalhousie KO +32CMK6KO Dalhousie KO +33CMK6WT Dalhousie WT +34CMK6KO Dalhousie KO +36CMK6WT Dalhousie WT +81CHE6WT PaloAlto WT +82CHE6WT PaloAlto WT +84CHE6KO PaloAlto KO +86CHE6WT PaloAlto WT +87CHE6KO PaloAlto KO +88CHE6KO PaloAlto KO +99CHE6KO PaloAlto KO +9CMK6KO Dalhousie KO
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/study_seqs_full.fasta Sat Mar 04 20:27:42 2023 +0000 @@ -0,0 +1,10 @@ +>02905cfb87861c837dde629596d9272b +TGGTCTTGACATCCCTCTGACGAGTGAGTAATGTCGCTTTCCCTTCGGGGCAGAGGAGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCTTTAGTAGCCAGCAGTAAGATGGGAACTCTAGAGAGACTGCCGGGGATAACCCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGACCAGGGCTACACACGTGCTACAATGGCGTAAACAGAGGGAAGCGACCCTGTGAAGGTAAGCAAATCCCAAAAATAACGTCTCAGTTCGGATTGTAGTCTGCAACTCGACTACATGAAGCTGGAATCGCTAGTAATCGCGAATCAGAATGTCGCGGTGAATACGTTCCCGG +>03562a221b15ef37470e4567e112f35f +CGGGCTTGAAAGTTAGTGACCGGAGATGAAAGTCTCCTTTCTATAGCAATATAGACACGAAACTAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCTTTTCTTCAGTTACCATCATTAAGTTGGGGACTCTGAAGACACTGCCATCGTAAGATGTGAGGAAGGATGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCGACACACGTGTTACAATGGCGTGGACAGCGGGGAACGAGGTGGCGACACCGAGGGAATCCCGAAACCACGTCCCAGTTCGGATTGGAGTCTGCAACTCGACTCCATGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCATGGCGCGGTGAATACGTTC +>03af6a6644bc358ee6716cbb44a5a479 +AGGGCTTGACATATATCAGAATATACTAGAGATAGTATAGTCCTTCGGGACTGATATACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGTCCTTAGTTGCCAGCACGTAAAGGTGGGAACTCTAAGGAGACTGCCGGTGATAAATCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCTTTATGTCCTGGGCTACACACGTACTACAATGGCCGTGACAGAGAGAAACGAAACAGTGATGTGGAGTAAAACTCTAAAAGCGGTCTCAGTTCGGATTGAAGGCTGAAATTCGCCTTCATGAAGCTGGAATTGCTAGTAATGGCAGGTCAGCATACTGCCGTGAATACGTTCCCGG +>03cb13abd3f1c5444360e489460bdfb0 +CGGGCTCAAACGGAAGGGGACGGATTGTGAAAGCAGTCTTTCCTTCGGGACCGCTTCCGAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCCTACCGACAGTTGCTAACAGATTAAGCTGAGGACTCTGTCGGGACTGCCGGCGCAAGCTGTGAGGAAGGCGGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCGACACACGTGTTACAATGGCAGGTACAGCGGGAAGCCACCCGGCGACGGGGCGCGGAACCCGAAAACCTGTCTCAGTTCGGATTGGAGTCTGCAACCCGACTCCATGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCACGGCGCGGTGAATACGTTCCCG +>05f9281835817fddd06162cd69497a2d +CGGGCTTAAATTGCATCTGAATGATTTGGAAACAGATCAGCCGCAAGGCAGATGTGAAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCTTGCTGTCAGTTACTAACAGGTCATGCTGAGGACTCTGACGGGACTGCCATCGTAAGATGTGAGGAAGGTGGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCTACACACGTGTTACAATGGGGGGTACAGCAGGCAGCTACCTGGCGACAGGATGCTAATCCCGAAAGCCCCTCTCAGTTCGGATTGGAGTCTGCAACCCGACTCCATGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCACGGCGCGGTGAATACGTTCCCGGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/study_seqs_test.fasta Sat Mar 04 20:27:42 2023 +0000 @@ -0,0 +1,10 @@ +>02905cfb87861c837dde629596d9272b +TGGTCTTGACATCCCTCTGACGAGTGAGTAATGTCGCTTTCCCTTCGGGGCAGAGGAGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCTTTAGTAGCCAGCAGTAAGATGGGAACTCTAGAGAGACTGCCGGGGATAACCCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGACCAGGGCTACACACGTGCTACAATGGCGTAAACAGAGGGAAGCGACCCTGTGAAGGTAAGCAAATCCCAAAAATAACGTCTCAGTTCGGATTGTAGTCTGCAACTCGACTACATGAAGCTGGAATCGCTAGTAATCGCGAATCAGAATGTCGCGGTGAATACGTTCCCGG +>03562a221b15ef37470e4567e112f35f +CGGGCTTGAAAGTTAGTGACCGGAGATGAAAGTCTCCTTTCTATAGCAATATAGACACGAAACTAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCTTTTCTTCAGTTACCATCATTAAGTTGGGGACTCTGAAGACACTGCCATCGTAAGATGTGAGGAAGGATGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCGACACACGTGTTACAATGGCGTGGACAGCGGGGAACGAGGTGGCGACACCGAGGGAATCCCGAAACCACGTCCCAGTTCGGATTGGAGTCTGCAACTCGACTCCATGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCATGGCGCGGTGAATACGTTC +>03af6a6644bc358ee6716cbb44a5a479 +AGGGCTTGACATATATCAGAATATACTAGAGATAGTATAGTCCTTCGGGACTGATATACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGTCCTTAGTTGCCAGCACGTAAAGGTGGGAACTCTAAGGAGACTGCCGGTGATAAATCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCTTTATGTCCTGGGCTACACACGTACTACAATGGCCGTGACAGAGAGAAACGAAACAGTGATGTGGAGTAAAACTCTAAAAGCGGTCTCAGTTCGGATTGAAGGCTGAAATTCGCCTTCATGAAGCTGGAATTGCTAGTAATGGCAGGTCAGCATACTGCCGTGAATACGTTCCCGG +>03cb13abd3f1c5444360e489460bdfb0 +CGGGCTCAAACGGAAGGGGACGGATTGTGAAAGCAGTCTTTCCTTCGGGACCGCTTCCGAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCCTACCGACAGTTGCTAACAGATTAAGCTGAGGACTCTGTCGGGACTGCCGGCGCAAGCTGTGAGGAAGGCGGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCGACACACGTGTTACAATGGCAGGTACAGCGGGAAGCCACCCGGCGACGGGGCGCGGAACCCGAAAACCTGTCTCAGTTCGGATTGGAGTCTGCAACCCGACTCCATGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCACGGCGCGGTGAATACGTTCCCG +>05f9281835817fddd06162cd69497a2d +CGGGCTTAAATTGCATCTGAATGATTTGGAAACAGATCAGCCGCAAGGCAGATGTGAAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCTTGCTGTCAGTTACTAACAGGTCATGCTGAGGACTCTGACGGGACTGCCATCGTAAGATGTGAGGAAGGTGGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCTACACACGTGTTACAATGGGGGGTACAGCAGGCAGCTACCTGGCGACAGGATGCTAATCCCGAAAGCCCCTCTCAGTTCGGATTGGAGTCTGCAACCCGACTCCATGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCACGGCGCGGTGAATACGTTCCCGGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/study_seqs_test2.fasta Sat Mar 04 20:27:42 2023 +0000 @@ -0,0 +1,10 @@ +>02905cfb87861c837dde629596d9272b +TGGTCTTGACATCCCTCTGACGAGTGAGTAATGTCGCTTTCCCTTCGGGGCAGAGGAGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCTTTAGTAGCCAGCAGTAAGATGGGAACTCTAGAGAGACTGCCGGGGATAACCCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGACCAGGGCTACACACGTGCTACAATGGCGTAAACAGAGGGAAGCGACCCTGTGAAGGTAAGCAAATCCCAAAAATAACGTCTCAGTTCGGATTGTAGTCTGCAACTCGACTACATGAAGCTGGAATCGCTAGTAATCGCGAATCAGAATGTCGCGGTGAATACGTTCCCGG +>03562a221b15ef37470e4567e112f35f +CGGGCTTGAAAGTTAGTGACCGGAGATGAAAGTCTCCTTTCTATAGCAATATAGACACGAAACTAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCTTTTCTTCAGTTACCATCATTAAGTTGGGGACTCTGAAGACACTGCCATCGTAAGATGTGAGGAAGGATGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCGACACACGTGTTACAATGGCGTGGACAGCGGGGAACGAGGTGGCGACACCGAGGGAATCCCGAAACCACGTCCCAGTTCGGATTGGAGTCTGCAACTCGACTCCATGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCATGGCGCGGTGAATACGTTC +>03af6a6644bc358ee6716cbb44a5a479 +AGGGCTTGACATATATCAGAATATACTAGAGATAGTATAGTCCTTCGGGACTGATATACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGTCCTTAGTTGCCAGCACGTAAAGGTGGGAACTCTAAGGAGACTGCCGGTGATAAATCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCTTTATGTCCTGGGCTACACACGTACTACAATGGCCGTGACAGAGAGAAACGAAACAGTGATGTGGAGTAAAACTCTAAAAGCGGTCTCAGTTCGGATTGAAGGCTGAAATTCGCCTTCATGAAGCTGGAATTGCTAGTAATGGCAGGTCAGCATACTGCCGTGAATACGTTCCCGG +>03cb13abd3f1c5444360e489460bdfb0 +CGGGCTCAAACGGAAGGGGACGGATTGTGAAAGCAGTCTTTCCTTCGGGACCGCTTCCGAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCCTACCGACAGTTGCTAACAGATTAAGCTGAGGACTCTGTCGGGACTGCCGGCGCAAGCTGTGAGGAAGGCGGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCGACACACGTGTTACAATGGCAGGTACAGCGGGAAGCCACCCGGCGACGGGGCGCGGAACCCGAAAACCTGTCTCAGTTCGGATTGGAGTCTGCAACCCGACTCCATGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCACGGCGCGGTGAATACGTTCCCG +>05f9281835817fddd06162cd69497a2d +CGGGCTTAAATTGCATCTGAATGATTTGGAAACAGATCAGCCGCAAGGCAGATGTGAAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCTTGCTGTCAGTTACTAACAGGTCATGCTGAGGACTCTGACGGGACTGCCATCGTAAGATGTGAGGAAGGTGGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCTACACACGTGTTACAATGGGGGGTACAGCAGGCAGCTACCTGGCGACAGGATGCTAATCCCGAAAGCCCCTCTCAGTTCGGATTGGAGTCTGCAACCCGACTCCATGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCACGGCGCGGTGAATACGTTCCCGGG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/table.mothur.shared Sat Mar 04 20:27:42 2023 +0000 @@ -0,0 +1,25 @@ +label Group numOtus 86681c8e9c64b6683071cf185f9e3419 663baa27cddeac43b08f428e96650bf5 abd40160e03332710641ee74b1b42816 bac85f511e578b92b4a16264719bdb2d 2a45f0b7f68a35504402988bcb8eb7fe 8db33d54e5184b0f448ae140f793368a 40c2346925c479d2f90d76aea73b0975 cebb9cfc1d8430f13650adacf98b0a61 d307aef8086bbdb1c3e4f3d5511412dc 23fe12a325dfefcdb23447f43b6b896e daac2b933e609bc0b483a4c25c92a055 de1be320837d0ac367b4ccef7f7ef44c c6f8879689d204423d60258f2759ebf1 749f091c6dfc58f7a48d89cf4c0f3049 7e5d7cc681f5a0c25e0816a77d59ffb2 c9e3a646d6b14e727ec78e0abe6aa878 ff33233ffebbe6e3720af8bba7e89f08 f5b23f626e3f2d2d1213f83c6de3e385 48292bb527301239168556057a7805bb 343635a5abc8d3b1dbd2b305eb0efe32 9272935a83a4b015099938a373d42cc5 48634a509c9db2a42174d1920e5c3999 a895f151de7f3a3e9b84e15800425631 e6380dc8bedb392a5c2139c21c26a7e4 6d5af1db8934361889a6fb8d80c70836 20e568023c10eaac834f1c110aacea18 cfe4029cc35d2695cf0ce8c5ff332956 d6cecaaf52a711cc96417a5334067830 691eeed271e420c8e7a91d5ea0cf5431 b639d3575f66b7b6b5dd908999072997 5c5f6d5a2d45a21bc576e475985efa17 288c8176059111c4c7fdfb0cd5afce64 94be7094bb21b6425f166ebb9f64f64f 8726f3950f95ade7a06f46b7cf3de779 763af2e6cfd1d573893fa6d28aafc4b5 b8083ad94a9a412e5d124d68d2da3343 f3e89fa547a772288e6624c88135a47f +userLabel 100CHE6KO 37 716 112 0 56 0 0 3 0 11 108 0 2 27 75 10 0 239 67 0 64 0 73 289 286 308 26 69 186 107 134 35 102 34 111 89 112 0 +userLabel 101CHE6WT 37 699 29 0 4 0 0 19 0 69 0 0 0 37 0 26 9 215 41 0 25 0 81 896 0 242 517 238 267 135 51 58 90 51 166 110 0 0 +userLabel 102CHE6WT 37 408 45 0 63 0 0 0 0 32 116 0 0 7 7 17 9 145 17 0 13 0 229 342 218 187 230 110 17 102 58 25 59 48 54 91 0 0 +userLabel 103CHE6KO 37 580 35 0 131 0 0 0 0 26 121 0 0 27 55 19 6 184 13 0 26 0 10 340 258 214 144 110 90 67 71 87 69 76 0 93 776 0 +userLabel 104CHE6KO 37 958 75 0 90 0 0 7 0 49 125 0 0 12 23 25 6 330 14 0 69 0 0 468 235 339 255 117 158 183 117 103 94 133 39 142 21 0 +userLabel 20CMK6KO 37 1137 283 144 440 50 65 67 168 92 181 81 157 25 14 38 85 100 92 136 25 50 441 0 0 0 0 0 0 5 0 0 0 0 0 0 0 273 +userLabel 21CMK6WT 37 1806 432 67 459 15 11 36 81 42 91 96 214 50 92 48 139 191 34 161 48 62 94 0 0 0 0 0 0 5 0 0 0 0 0 0 0 79 +userLabel 22CMK6KO 37 2158 536 301 352 170 78 351 237 308 530 62 64 142 21 96 387 225 69 237 26 605 170 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 +userLabel 23CMK6WT 37 1858 873 95 456 37 19 23 108 14 501 78 6 12 19 31 150 311 23 154 39 406 79 0 0 0 0 0 0 12 0 0 0 0 0 0 0 306 +userLabel 24CMK6KO 37 1964 819 292 426 275 251 353 135 325 941 92 76 124 173 110 111 197 99 224 56 349 489 0 0 0 0 0 0 0 0 0 0 0 0 0 0 41 +userLabel 26CMK6WT 37 1041 372 90 511 172 136 154 70 178 240 174 26 100 109 48 108 109 147 115 78 351 346 0 0 0 0 0 0 21 0 0 0 0 0 0 0 0 +userLabel 30CMK6KO 37 1899 457 315 462 32 0 8 20 11 19 98 291 118 146 85 170 167 69 212 29 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 2654 516 +userLabel 32CMK6KO 37 540 495 283 455 284 76 10 212 9 50 101 203 110 37 77 235 36 122 47 23 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 436 +userLabel 33CMK6WT 37 1716 411 245 372 224 16 144 66 191 284 163 80 50 16 38 20 149 72 162 24 317 209 0 0 0 0 0 0 0 0 0 0 0 0 0 32 0 +userLabel 34CMK6KO 37 625 338 285 415 61 72 9 134 2 7 101 162 28 69 56 64 48 112 49 22 71 2 0 0 0 0 0 0 0 0 0 0 0 0 0 197 563 +userLabel 36CMK6WT 37 1314 553 119 294 189 111 262 31 278 699 96 13 52 13 55 47 84 125 111 22 340 109 0 0 0 0 0 0 6 0 0 0 0 0 0 0 13 +userLabel 81CHE6WT 37 872 28 0 89 0 64 31 0 155 179 0 7 56 81 45 10 206 16 0 84 0 13 265 219 265 43 83 106 95 243 103 63 134 29 94 0 0 +userLabel 82CHE6WT 37 766 33 0 37 0 48 23 0 107 261 0 0 55 12 38 25 164 17 0 55 0 40 407 312 166 24 147 84 68 234 126 111 133 92 52 0 0 +userLabel 84CHE6KO 37 695 27 0 122 0 102 28 0 157 480 0 3 102 10 49 49 180 33 0 67 0 37 347 562 192 48 104 76 108 409 164 115 199 131 47 0 0 +userLabel 86CHE6WT 37 1114 88 0 35 0 0 5 0 47 209 0 0 9 27 23 12 302 47 0 105 0 167 136 498 272 3 47 118 176 88 79 84 98 85 103 0 0 +userLabel 87CHE6KO 37 1030 75 0 35 0 0 6 0 38 265 0 11 21 23 24 10 296 57 0 111 0 246 169 661 252 19 59 121 161 188 154 96 177 42 119 0 0 +userLabel 88CHE6KO 37 852 73 0 9 0 0 7 0 42 127 0 11 21 174 10 6 173 25 0 105 0 11 108 221 284 3 33 108 114 65 123 52 96 44 72 0 0 +userLabel 99CHE6KO 37 1160 113 0 138 0 0 23 0 67 124 0 8 34 131 38 2 297 117 0 80 0 15 523 320 385 206 150 202 128 85 74 166 59 211 106 17 0 +userLabel 9CMK6KO 37 852 223 137 269 74 36 141 47 157 678 78 39 52 22 38 48 50 43 79 13 8 319 0 0 0 0 0 0 25 0 0 0 0 0 0 3 17