# HG changeset patch
# User iuc
# Date 1677961678 0
# Node ID 6034c3f3ecf0edf4f9b0692ca476541ca367a720

planemo upload for repository https://github.com/picrust/picrust2 commit 972784d909912af20cd213fc56830fee79d83ca6

diff -r 000000000000 -r 6034c3f3ecf0 add_descriptions.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/add_descriptions.xml	Sat Mar 04 20:27:58 2023 +0000
@@ -0,0 +1,96 @@
+<tool id="picrust2_add_descriptions" name="PICRUSt2 Add descriptions" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>column to a function abundance table</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="bio_tool"/>
+    <expand macro="requirements"/>
+    <version_command>add_descriptions.py -v</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+add_descriptions.py
+    --input '$input'
+    --output '$func_abun_table_description'
+#if $map_file.selector == "default"
+    --map_type '$map_file.map_type'
+#else if $map_file.selector == "custom"
+    --custom_map_table '$map_file.custom_map_table'
+#end if
+    ]]></command>
+    <inputs>
+        <param argument="--input" type="data" format="tabular" label="Input function (gene family or pathway) abundance table"/>
+        <conditional name="map_file">
+            <param name="selector" type="select" label="Argument specifying non-default reference files to use for sequence placement">
+                <option value="default" selected="true">Default mapping file</option>
+                <option value="custom">Customized mapping file</option>
+            </param>
+            <when value="default">
+                <param argument="--map_type" type="select" label="Mapping table to use">
+                    <option value="COG">Clusters of Orthologous Genes database (COG)</option>
+                    <option value="EC">Enzyme Commission number database (EC number)</option>
+                    <option value="KO">KEGG Orthology database (KO)</option>
+                    <option value="PFAM">Pfam database</option>
+                    <option value="TIGRFAM">TIGRFAM database</option>
+                    <option value="METACYC">Metabolic Pathway database (MetaCyc)</option>
+                </param>
+            </when>
+            <when value="custom">
+                <param argument="--custom_map_table" type="data" format="tabular" label="Custom mapping table" help="A table with at least two columns linking function ids to descriptions for each function">
+                    <validator type="dataset_metadata_in_range" metadata_name="columns" min="2" message="Input needs to have at least two columns"/>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="func_abun_table_description" format="tabular" from_work_dir="added_description.tsv"/>
+    </outputs>
+    <tests>
+    <test expect_num_outputs="1">
+        <param name="input" value="pred_metagenome_unstrat.tsv.gz"/>
+        <conditional name="map_file">
+            <param name="selector" value="default"/>
+            <param name="map_type" value="EC"/>
+        </conditional>
+        <output name="func_abun_table_description">
+            <assert_contents>
+                <has_text text="description"/>
+                <has_n_lines n="1000"/>
+            </assert_contents>
+        </output>
+    </test>
+    <test expect_num_outputs="1">
+        <param name="input" value="pred_metagenome_unstrat.tsv.gz"/>
+        <conditional name="map_file">
+            <param name="selector" value="custom"/>
+            <param name="custom_map_table" value="ec_unstrat_test.txt.gz"/>
+        </conditional>
+        <output name="func_abun_table_description">
+            <assert_contents>
+                <has_text text="description"/>
+                <has_n_lines n="1000"/>
+            </assert_contents>
+        </output>
+    </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+Add Descriptions
+================
+Adds a description column to a function abundance table and outputs a new file.
+
+Note
+====
+The user needs to specify the input file and what type of functions are in the input table. Will throw an error if no ids overlap and otherwise will fill in "not_found" for the description of ids in the function table not in the mapfile.
+
+Input
+=====
+Input function abundance table.
+
+Output
+======
+Output function abundance table with added description column.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1038/s41587-020-0548-6</citation>
+    </citations>
+</tool>
\ No newline at end of file
diff -r 000000000000 -r 6034c3f3ecf0 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Sat Mar 04 20:27:58 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
diff -r 000000000000 -r 6034c3f3ecf0 test-data/16S_predicted_and_nsti.tsv.gz
Binary file test-data/16S_predicted_and_nsti.tsv.gz has changed
diff -r 000000000000 -r 6034c3f3ecf0 test-data/EC_predicted.tsv.gz
Binary file test-data/EC_predicted.tsv.gz has changed
diff -r 000000000000 -r 6034c3f3ecf0 test-data/ec_unstrat_test.txt.gz
Binary file test-data/ec_unstrat_test.txt.gz has changed
diff -r 000000000000 -r 6034c3f3ecf0 test-data/img_centroid_16S_aligned_head30.fna.gz
Binary file test-data/img_centroid_16S_aligned_head30.fna.gz has changed
diff -r 000000000000 -r 6034c3f3ecf0 test-data/img_centroid_16S_aligned_head30.hmm
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/img_centroid_16S_aligned_head30.hmm	Sat Mar 04 20:27:58 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 - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.05789  3.57112  3.57112  1.46634  0.26236  0.38546  1.13987
+      5   2.26480  2.65592  0.30114  2.45412     47 g - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.05291  3.65865  3.65865  1.46634  0.26236  1.09861  0.40547
+      6   2.31076  0.40279  2.41667  1.94391     48 c - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.05291  3.65865  3.65865  1.46634  0.26236  1.09861  0.40547
+      7   2.26480  2.65592  0.30114  2.45412     49 g - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.05291  3.65865  3.65865  1.46634  0.26236  1.09861  0.40547
+      8   1.40350  1.84283  0.86745  1.73799     50 g - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.05291  3.65865  3.65865  1.46634  0.26236  1.09861  0.40547
+      9   0.35395  2.43840  2.24483  2.25526     51 a - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.05291  3.65865  3.65865  1.46634  0.26236  1.09861  0.40547
+     10   2.31076  0.40279  2.41667  1.94391     52 c - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.05291  3.65865  3.65865  1.46634  0.26236  1.09861  0.40547
+     11   2.26480  2.65592  0.30114  2.45412     53 g - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.05291  3.65865  3.65865  1.46634  0.26236  1.09861  0.40547
+     12   2.26480  2.65592  0.30114  2.45412     54 g - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.05291  3.65865  3.65865  1.46634  0.26236  1.09861  0.40547
+     13   2.26480  2.65592  0.30114  2.45412     55 g - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.05291  3.65865  3.65865  1.46634  0.26236  1.09861  0.40547
+     14   2.18399  2.01659  2.27039  0.42920     56 t - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.05291  3.65865  3.65865  1.46634  0.26236  1.09861  0.40547
+     15   2.26480  2.65592  0.30114  2.45412     57 g - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.05291  3.65865  3.65865  1.46634  0.26236  1.09861  0.40547
+     16   0.35395  2.43840  2.24483  2.25526     58 a - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.05291  3.65865  3.65865  1.46634  0.26236  1.09861  0.40547
+     17   2.26480  2.65592  0.30114  2.45412     59 g - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.05291  3.65865  3.65865  1.46634  0.26236  1.09861  0.40547
+     18   2.18399  2.01659  2.27039  0.42920     60 t - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.05291  3.65865  3.65865  1.46634  0.26236  1.09861  0.40547
+     19   0.35395  2.43840  2.24483  2.25526     61 a - - -
+          1.38629  1.38629  1.38629  1.38629
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+     20   0.35395  2.43840  2.24483  2.25526     62 a - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.05291  3.65865  3.65865  1.46634  0.26236  1.09861  0.40547
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+          1.38629  1.38629  1.38629  1.38629
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+          1.38629  1.38629  1.38629  1.38629
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+          1.38629  1.38629  1.38629  1.38629
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+          1.38629  1.38629  1.38629  1.38629
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+          1.38629  1.38629  1.38629  1.38629
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+          1.38629  1.38629  1.38629  1.38629
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+          1.38629  1.38629  1.38629  1.38629
+          0.05291  3.65865  3.65865  1.46634  0.26236  1.09861  0.40547
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+          1.38629  1.38629  1.38629  1.38629
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+          1.38629  1.38629  1.38629  1.38629
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+     31   0.35395  2.43840  2.24483  2.25526     73 a - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.05291  3.65865  3.65865  1.46634  0.26236  1.09861  0.40547
+     32   1.37215  1.25103  1.81122  1.21479     74 t - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.11970  3.65865  2.44132  1.46634  0.26236  1.09861  0.40547
+     33   1.76383  0.64638  2.07292  1.72117     75 c - - -
+          1.38629  1.38629  1.38629  1.38629
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+          1.38629  1.38629  1.38629  1.38629
+          0.05291  3.65865  3.65865  1.46634  0.26236  1.09861  0.40547
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+          1.38629  1.38629  1.38629  1.38629
+          0.05291  3.65865  3.65865  1.46634  0.26236  1.09861  0.40547
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+          1.38629  1.38629  1.38629  1.38629
+          0.05291  3.65865  3.65865  1.46634  0.26236  1.09861  0.40547
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+          1.38629  1.38629  1.38629  1.38629
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+          1.38629  1.38629  1.38629  1.38629
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+          1.38629  1.38629  1.38629  1.38629
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+          1.38629  1.38629  1.38629  1.38629
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+          1.38629  1.38629  1.38629  1.38629
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+          1.38629  1.38629  1.38629  1.38629
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+          1.38629  1.38629  1.38629  1.38629
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+          1.38629  1.38629  1.38629  1.38629
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+          1.38629  1.38629  1.38629  1.38629
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+   1212   1.77113  1.21984  1.83225  0.98208   1259 t - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.06597  3.44458  3.44458  1.46634  0.26236  2.34938  0.10029
+   1213   1.88494  1.75948  1.92667  0.63413   1260 t - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.06597  3.44458  3.44458  1.46634  0.26236  2.34938  0.10029
+   1214   1.94221  2.21786  0.48684  2.01586   1261 g - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.06597  3.44458  3.44458  1.46634  0.26236  2.34938  0.10029
+   1215   1.94221  2.21786  0.48684  2.01586   1262 g - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.06597  3.44458  3.44458  1.46634  0.26236  2.34938  0.10029
+   1216   1.94221  2.21786  0.48684  2.01586   1263 g - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.06597  3.44458  3.44458  1.46634  0.26236  2.34938  0.10029
+   1217   1.94221  2.21786  0.48684  2.01586   1264 g - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.06597  3.44458  3.44458  1.46634  0.26236  2.34938  0.10029
+   1218   1.88494  1.75948  1.92667  0.63413   1265 t - - -
+          1.38629  1.38629  1.38629  1.38629
+          0.06597  3.44458  3.44458  1.46634  0.26236  2.34938  0.10029
+   1219   1.94221  2.21786  0.48684  2.01586   1266 g - - -
+          1.09892  1.67037  1.28581  1.59867
+          0.35693  1.20338        *  2.84032  0.06018  0.00000        *
+//
diff -r 000000000000 -r 6034c3f3ecf0 test-data/img_centroid_16S_aligned_head30.model
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/img_centroid_16S_aligned_head30.model	Sat Mar 04 20:27:58 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
diff -r 000000000000 -r 6034c3f3ecf0 test-data/img_centroid_16S_aligned_head30.tre
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/img_centroid_16S_aligned_head30.tre	Sat Mar 04 20:27:58 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;
diff -r 000000000000 -r 6034c3f3ecf0 test-data/known_traits.tsv.gz
Binary file test-data/known_traits.tsv.gz has changed
diff -r 000000000000 -r 6034c3f3ecf0 test-data/metadata.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/metadata.tsv	Sat Mar 04 20:27:58 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
diff -r 000000000000 -r 6034c3f3ecf0 test-data/out_tree.zip
Binary file test-data/out_tree.zip has changed
diff -r 000000000000 -r 6034c3f3ecf0 test-data/per_seq_func.tsv.gz
Binary file test-data/per_seq_func.tsv.gz has changed
diff -r 000000000000 -r 6034c3f3ecf0 test-data/pred_metagenome_strat.tsv.gz
Binary file test-data/pred_metagenome_strat.tsv.gz has changed
diff -r 000000000000 -r 6034c3f3ecf0 test-data/pred_metagenome_unstrat.tsv.gz
Binary file test-data/pred_metagenome_unstrat.tsv.gz has changed
diff -r 000000000000 -r 6034c3f3ecf0 test-data/seqtab_norm.tsv.gz
Binary file test-data/seqtab_norm.tsv.gz has changed
diff -r 000000000000 -r 6034c3f3ecf0 test-data/study_seqs_full.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/study_seqs_full.fasta	Sat Mar 04 20:27:58 2023 +0000
@@ -0,0 +1,10 @@
+>02905cfb87861c837dde629596d9272b
+TGGTCTTGACATCCCTCTGACGAGTGAGTAATGTCGCTTTCCCTTCGGGGCAGAGGAGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCTTTAGTAGCCAGCAGTAAGATGGGAACTCTAGAGAGACTGCCGGGGATAACCCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGACCAGGGCTACACACGTGCTACAATGGCGTAAACAGAGGGAAGCGACCCTGTGAAGGTAAGCAAATCCCAAAAATAACGTCTCAGTTCGGATTGTAGTCTGCAACTCGACTACATGAAGCTGGAATCGCTAGTAATCGCGAATCAGAATGTCGCGGTGAATACGTTCCCGG
+>03562a221b15ef37470e4567e112f35f
+CGGGCTTGAAAGTTAGTGACCGGAGATGAAAGTCTCCTTTCTATAGCAATATAGACACGAAACTAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCTTTTCTTCAGTTACCATCATTAAGTTGGGGACTCTGAAGACACTGCCATCGTAAGATGTGAGGAAGGATGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCGACACACGTGTTACAATGGCGTGGACAGCGGGGAACGAGGTGGCGACACCGAGGGAATCCCGAAACCACGTCCCAGTTCGGATTGGAGTCTGCAACTCGACTCCATGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCATGGCGCGGTGAATACGTTC
+>03af6a6644bc358ee6716cbb44a5a479
+AGGGCTTGACATATATCAGAATATACTAGAGATAGTATAGTCCTTCGGGACTGATATACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGTCCTTAGTTGCCAGCACGTAAAGGTGGGAACTCTAAGGAGACTGCCGGTGATAAATCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCTTTATGTCCTGGGCTACACACGTACTACAATGGCCGTGACAGAGAGAAACGAAACAGTGATGTGGAGTAAAACTCTAAAAGCGGTCTCAGTTCGGATTGAAGGCTGAAATTCGCCTTCATGAAGCTGGAATTGCTAGTAATGGCAGGTCAGCATACTGCCGTGAATACGTTCCCGG
+>03cb13abd3f1c5444360e489460bdfb0
+CGGGCTCAAACGGAAGGGGACGGATTGTGAAAGCAGTCTTTCCTTCGGGACCGCTTCCGAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCCTACCGACAGTTGCTAACAGATTAAGCTGAGGACTCTGTCGGGACTGCCGGCGCAAGCTGTGAGGAAGGCGGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCGACACACGTGTTACAATGGCAGGTACAGCGGGAAGCCACCCGGCGACGGGGCGCGGAACCCGAAAACCTGTCTCAGTTCGGATTGGAGTCTGCAACCCGACTCCATGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCACGGCGCGGTGAATACGTTCCCG
+>05f9281835817fddd06162cd69497a2d
+CGGGCTTAAATTGCATCTGAATGATTTGGAAACAGATCAGCCGCAAGGCAGATGTGAAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCTTGCTGTCAGTTACTAACAGGTCATGCTGAGGACTCTGACGGGACTGCCATCGTAAGATGTGAGGAAGGTGGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCTACACACGTGTTACAATGGGGGGTACAGCAGGCAGCTACCTGGCGACAGGATGCTAATCCCGAAAGCCCCTCTCAGTTCGGATTGGAGTCTGCAACCCGACTCCATGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCACGGCGCGGTGAATACGTTCCCGGG
diff -r 000000000000 -r 6034c3f3ecf0 test-data/study_seqs_test.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/study_seqs_test.fasta	Sat Mar 04 20:27:58 2023 +0000
@@ -0,0 +1,10 @@
+>02905cfb87861c837dde629596d9272b
+TGGTCTTGACATCCCTCTGACGAGTGAGTAATGTCGCTTTCCCTTCGGGGCAGAGGAGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCTTTAGTAGCCAGCAGTAAGATGGGAACTCTAGAGAGACTGCCGGGGATAACCCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGACCAGGGCTACACACGTGCTACAATGGCGTAAACAGAGGGAAGCGACCCTGTGAAGGTAAGCAAATCCCAAAAATAACGTCTCAGTTCGGATTGTAGTCTGCAACTCGACTACATGAAGCTGGAATCGCTAGTAATCGCGAATCAGAATGTCGCGGTGAATACGTTCCCGG
+>03562a221b15ef37470e4567e112f35f
+CGGGCTTGAAAGTTAGTGACCGGAGATGAAAGTCTCCTTTCTATAGCAATATAGACACGAAACTAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCTTTTCTTCAGTTACCATCATTAAGTTGGGGACTCTGAAGACACTGCCATCGTAAGATGTGAGGAAGGATGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCGACACACGTGTTACAATGGCGTGGACAGCGGGGAACGAGGTGGCGACACCGAGGGAATCCCGAAACCACGTCCCAGTTCGGATTGGAGTCTGCAACTCGACTCCATGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCATGGCGCGGTGAATACGTTC
+>03af6a6644bc358ee6716cbb44a5a479
+AGGGCTTGACATATATCAGAATATACTAGAGATAGTATAGTCCTTCGGGACTGATATACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGTCCTTAGTTGCCAGCACGTAAAGGTGGGAACTCTAAGGAGACTGCCGGTGATAAATCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCTTTATGTCCTGGGCTACACACGTACTACAATGGCCGTGACAGAGAGAAACGAAACAGTGATGTGGAGTAAAACTCTAAAAGCGGTCTCAGTTCGGATTGAAGGCTGAAATTCGCCTTCATGAAGCTGGAATTGCTAGTAATGGCAGGTCAGCATACTGCCGTGAATACGTTCCCGG
+>03cb13abd3f1c5444360e489460bdfb0
+CGGGCTCAAACGGAAGGGGACGGATTGTGAAAGCAGTCTTTCCTTCGGGACCGCTTCCGAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCCTACCGACAGTTGCTAACAGATTAAGCTGAGGACTCTGTCGGGACTGCCGGCGCAAGCTGTGAGGAAGGCGGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCGACACACGTGTTACAATGGCAGGTACAGCGGGAAGCCACCCGGCGACGGGGCGCGGAACCCGAAAACCTGTCTCAGTTCGGATTGGAGTCTGCAACCCGACTCCATGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCACGGCGCGGTGAATACGTTCCCG
+>05f9281835817fddd06162cd69497a2d
+CGGGCTTAAATTGCATCTGAATGATTTGGAAACAGATCAGCCGCAAGGCAGATGTGAAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCTTGCTGTCAGTTACTAACAGGTCATGCTGAGGACTCTGACGGGACTGCCATCGTAAGATGTGAGGAAGGTGGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCTACACACGTGTTACAATGGGGGGTACAGCAGGCAGCTACCTGGCGACAGGATGCTAATCCCGAAAGCCCCTCTCAGTTCGGATTGGAGTCTGCAACCCGACTCCATGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCACGGCGCGGTGAATACGTTCCCGGG
diff -r 000000000000 -r 6034c3f3ecf0 test-data/study_seqs_test2.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/study_seqs_test2.fasta	Sat Mar 04 20:27:58 2023 +0000
@@ -0,0 +1,10 @@
+>02905cfb87861c837dde629596d9272b
+TGGTCTTGACATCCCTCTGACGAGTGAGTAATGTCGCTTTCCCTTCGGGGCAGAGGAGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCTTTAGTAGCCAGCAGTAAGATGGGAACTCTAGAGAGACTGCCGGGGATAACCCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGACCAGGGCTACACACGTGCTACAATGGCGTAAACAGAGGGAAGCGACCCTGTGAAGGTAAGCAAATCCCAAAAATAACGTCTCAGTTCGGATTGTAGTCTGCAACTCGACTACATGAAGCTGGAATCGCTAGTAATCGCGAATCAGAATGTCGCGGTGAATACGTTCCCGG
+>03562a221b15ef37470e4567e112f35f
+CGGGCTTGAAAGTTAGTGACCGGAGATGAAAGTCTCCTTTCTATAGCAATATAGACACGAAACTAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCTTTTCTTCAGTTACCATCATTAAGTTGGGGACTCTGAAGACACTGCCATCGTAAGATGTGAGGAAGGATGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCGACACACGTGTTACAATGGCGTGGACAGCGGGGAACGAGGTGGCGACACCGAGGGAATCCCGAAACCACGTCCCAGTTCGGATTGGAGTCTGCAACTCGACTCCATGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCATGGCGCGGTGAATACGTTC
+>03af6a6644bc358ee6716cbb44a5a479
+AGGGCTTGACATATATCAGAATATACTAGAGATAGTATAGTCCTTCGGGACTGATATACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGTCCTTAGTTGCCAGCACGTAAAGGTGGGAACTCTAAGGAGACTGCCGGTGATAAATCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCTTTATGTCCTGGGCTACACACGTACTACAATGGCCGTGACAGAGAGAAACGAAACAGTGATGTGGAGTAAAACTCTAAAAGCGGTCTCAGTTCGGATTGAAGGCTGAAATTCGCCTTCATGAAGCTGGAATTGCTAGTAATGGCAGGTCAGCATACTGCCGTGAATACGTTCCCGG
+>03cb13abd3f1c5444360e489460bdfb0
+CGGGCTCAAACGGAAGGGGACGGATTGTGAAAGCAGTCTTTCCTTCGGGACCGCTTCCGAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCCTACCGACAGTTGCTAACAGATTAAGCTGAGGACTCTGTCGGGACTGCCGGCGCAAGCTGTGAGGAAGGCGGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCGACACACGTGTTACAATGGCAGGTACAGCGGGAAGCCACCCGGCGACGGGGCGCGGAACCCGAAAACCTGTCTCAGTTCGGATTGGAGTCTGCAACCCGACTCCATGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCACGGCGCGGTGAATACGTTCCCG
+>05f9281835817fddd06162cd69497a2d
+CGGGCTTAAATTGCATCTGAATGATTTGGAAACAGATCAGCCGCAAGGCAGATGTGAAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCTTGCTGTCAGTTACTAACAGGTCATGCTGAGGACTCTGACGGGACTGCCATCGTAAGATGTGAGGAAGGTGGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCTACACACGTGTTACAATGGGGGGTACAGCAGGCAGCTACCTGGCGACAGGATGCTAATCCCGAAAGCCCCTCTCAGTTCGGATTGGAGTCTGCAACCCGACTCCATGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCACGGCGCGGTGAATACGTTCCCGGG
diff -r 000000000000 -r 6034c3f3ecf0 test-data/table.biom
Binary file test-data/table.biom has changed
diff -r 000000000000 -r 6034c3f3ecf0 test-data/table.mothur.shared
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/table.mothur.shared	Sat Mar 04 20:27:58 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
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