Galaxy |

Changeset 0:6077821e8ae7 (2023-03-04)

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

added:
macros.xml
pathway_pipeline.xml
test-data/16S_predicted_and_nsti.tsv.gz
test-data/EC_predicted.tsv.gz
test-data/ec_unstrat_test.txt.gz
test-data/img_centroid_16S_aligned_head30.fna.gz
test-data/img_centroid_16S_aligned_head30.hmm
test-data/img_centroid_16S_aligned_head30.model
test-data/img_centroid_16S_aligned_head30.tre
test-data/known_traits.tsv.gz
test-data/metadata.tsv
test-data/out_tree.zip
test-data/per_seq_func.tsv.gz
test-data/pred_metagenome_strat.tsv.gz
test-data/pred_metagenome_unstrat.tsv.gz
test-data/seqtab_norm.tsv.gz
test-data/study_seqs_full.fasta
test-data/study_seqs_test.fasta
test-data/study_seqs_test2.fasta
test-data/table.biom
test-data/table.mothur.shared
test-data/weighted_nsti.tsv.gz
test-data/workflow_seq_abun.biom

diff -r 000000000000 -r 6077821e8ae7 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Sat Mar 04 20:27:27 2023 +0000

[

b'@@ -0,0 +1,344 @@\n+<?xml version="1.0"?>\n+<macros>\n+ <token name="@TOOL_VERSION@">2.5.1</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@PROFILE@">22.01</token>\n+ <xml name="bio_tool">\n+ <xrefs>\n+ <xref type="bio.tools">picrust2</xref>\n+ </xrefs>\n+ </xml>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">picrust2</requirement>\n+ <yield/>\n+ </requirements>\n+ </xml>\n+ <token name="@HELP_HEADER@">\n+What it does\n+============\n+\n+PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of\n+Unobserved States) is a tool for predicting functional abundances based only on\n+marker gene sequences.\n+\n+Read more about the tool: https://github.com/picrust/picrust2/wiki\n+ </token>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1038/s41587-020-0548-6</citation>\n+ </citations>\n+ </xml>\n+\n+\n+\n+ <token name="@VAR_ACCESS_FOO@"><![CDATA[\n+ ## in picrust2_pipeline the parameters are within a section or a\n+ ## conditional. in the separate sections they are not.\n+ ## this function allows unified access\n+ #def getVarCond($sec_cond, $var)\n+ #if $varExists($var)\n+ #return $getVar($var)\n+ #else if $varExists($sec_cond + "." + $var)\n+ #return $getVar($sec_cond + "." + $var)\n+ #else\n+ #return \n+ #end if\n+ #end def\n+ ]]></token>\n+\n+ \n+\n+ <token name="@PLACE_SEQS_PREPROCESSING@"><![CDATA[\n+ ## determine project dir which is something like /lib/python3.8/site-packages/picrust2/default_files/\n+ PROJECT_DIR=\\$(python -c \'from picrust2 import default; print(default.project_dir)\') &&\n+ REF_DIR_BASE=\\$PROJECT_DIR"/default_files/" &&\n+ #if $getVarCond("place_seqs_section", "ref_dir.selector") == "custom"\n+ mkdir -p custom/ &&\n+ ln -s \'$getVarCond("place_seqs_section", "ref_dir.custom_fna")\' custom/custom.fna &&\n+ ln -s \'$getVarCond("place_seqs_section", "ref_dir.custom_hmm")\' custom/custom.hmm &&\n+ #if $getVarCond("place_seqs_section", "placement_tool") == "epa-ng"\n+ ln -s \'$getVarCond("place_seqs_section", "ref_dir.custom_model")\' custom/custom.model &&\n+ #else if $getVarCond("place_seqs_section", "placement_tool")\n+ ln -s \'$getVarCond("place_seqs_section", "ref_dir.custom_model")\' custom/custom.raxml_info &&\n+ #end if\n+ ln -s \'$getVarCond("place_seqs_section", "ref_dir.custom_tre")\' custom/custom.tre &&\n+ #end if\n+ ]]></token>\n+ <token name="@PLACE_SEQS_PARAMS@"><![CDATA[\n+ --study_fasta \'$getVarCond("place_seqs_section", "study_fasta")\'\n+ --placement_tool \'$getVarCond("place_seqs_section", "placement_tool")\'\n+ ## set refdir (default is prokaryotic), even if the default will\n+ ## be treated internally as `"\\$REF_DIR_BASE"$ref_dir.selector`\n+ ## picrust2 will complain about non-default reference files\n+ ## specified with default pathway mapfile\n+ #if $getVarCond("place_seqs_section", "ref_dir.selector") == "custom"\n+ --ref_dir custom/\n+ #else if $getVarCond("place_seqs_section", "ref_dir.selector") != "prokaryotic/pro_ref/"\n+ --ref_dir "\\$REF_DIR_BASE"$getVarCond("place_seqs_section", "ref_dir.selector")\n+ #end if\n+ --min_align $getVarCond("place_seqs_section", "min_align")\n+ ]]></token>\n+ <xml name="place_seqs_params">\n+ <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"/>\n+ <param argument="--placement_tool" type="select" label="Placement tool" help="Used '..b' 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">\n+ <option value="--per_sequence_contrib">Yes</option>\n+ <option value="" selected="true">No</option>\n+ </param>\n+ <when value="--per_sequence_contrib">\n+ <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"/>\n+ <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"/>\n+ \n+ <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\n+ stratified tables since it is extremely memory intensive"/>\n+ </when>\n+ <when value=""/>\n+ </conditional>\n+ <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"/>\n+ </xml>\n+ <xml name="pathways_output" tokens="from_work_dir" token_label_suffix="">\n+ <data name="pathways_output" format="tabular" from_work_dir="@FROM_WORK_DIR@/pathways_out/path_abun_unstrat.tabular" label="${tool.name} on ${on_string}: Pathway abundances">\n+ <yield/>\n+ </data>\n+ <collection name="pathways_intermediate_output" type="list" label="${tool.name} on ${on_string}: Intermediate files @LABEL_SUFFIX@" >\n+ <discover_datasets pattern="__name_and_ext__" directory="@FROM_WORK_DIR@/intermediate/pathways/" format="tabular"/>\n+ <yield name="intermediate_filter"/>\n+ </collection>\n+ <data format="tabular" name="path_cov_unstrat" from_work_dir="@FROM_WORK_DIR@/pathways_out/path_cov_unstrat.tabular" label="${tool.name} on ${on_string}: Pathway coverage @LABEL_SUFFIX@" >\n+ <yield/>\n+ <yield name="coverage_filter"/>\n+ </data>\n+ <data format="tabular" name="path_abun_unstrat_per_seq" from_work_dir="@FROM_WORK_DIR@/pathways_out/path_abun_unstrat_per_seq.tabular" label="${tool.name} on ${on_string}: Pathway abundance unstratified per sequence @LABEL_SUFFIX@" >\n+ <yield/>\n+ <yield name="per_sequence_filter"/>\n+ </data>\n+ <data format="tabular" name="path_abun_predictions" from_work_dir="@FROM_WORK_DIR@/pathways_out/path_abun_predictions.tabular" label="${tool.name} on ${on_string}: Pathway abundance predictions @LABEL_SUFFIX@" >\n+ <yield/>\n+ <yield name="per_sequence_filter"/>\n+ </data>\n+ <data format="tabular" name="path_abun_contrib" from_work_dir="@FROM_WORK_DIR@/pathways_out/path_abun_contrib.tabular" label="${tool.name} on ${on_string}: Pathway abundance contributed @LABEL_SUFFIX@" >\n+ <yield/>\n+ <yield name="per_sequence_filter"/>\n+ </data>\n+ </xml>\n+</macros>\n\\ No newline at end of file\n'

diff -r 000000000000 -r 6077821e8ae7 pathway_pipeline.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/pathway_pipeline.xml Sat Mar 04 20:27:27 2023 +0000

[

b'@@ -0,0 +1,164 @@\n+<tool id="picrust2_pathway_pipeline" name="PICRUSt2 Pathway abundance inference" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n+ <description></description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="bio_tool"/>\n+ <expand macro="requirements"/>\n+ <version_command>pathway_pipeline.py -v</version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+@VAR_ACCESS_FOO@\n+#if $intermediate_check\n+ mkdir intermediate &&\n+#end if\n+\n+pathway_pipeline.py\n+ --input \'$input\'\n+ @PATHWAY_PIPELINE_PARAMS@\n+ #if $intermediate_check\n+ --intermediate \'intermediate/pathways/\'\n+ #end if\n+ --out_dir \'pathways_out\'\n+ --processes "\\${GALAXY_SLOTS:-1}"\n+\n+## gunzip all results and rename all tsv files to tabular to simplify discovery\n+#set find_paths="pathways_out"\n+#if $intermediate_check\n+ #set find_paths+=" intermediate"\n+#end if\n+&&\n+find $find_paths -name "*.gz" -exec gunzip {} \\;\n+&&\n+find $find_paths -name "*.tsv" -exec sh -c \'mv {} \\$(dirname {})/\\$(basename {} .tsv).tabular\' \\;\n+&&\n+## otherwise the `;` on the last line is swallowed\n+true\n+ ]]></command>\n+ <inputs>\n+ <param argument="--input" type="data" format="tabular" label="Input table with gene family abundances" help="Unstratified or stratified output of PICRUSt2 Metagenome prediction tool"/>\n+ <expand macro="pathway_pipeline_params" mapargument="--map"/>\n+ <param argument="--intermediate_check" type="boolean" truevalue="intermediate_check" falsevalue="" checked="false" label="Keep intermediate files" help="Intermediate output files will be deleted by default"/>\n+ </inputs>\n+ <outputs>\n+ <expand macro="pathways_output" from_work_dir="./">\n+ <token name="intermediate_filter">\n+ <filter>intermediate_check</filter>\n+ </token>\n+ <token name="coverage_filter">\n+ <filter>coverage</filter>\n+ </token>\n+ <token name="per_sequence_filter">\n+ <filter>strat_output[\'per_sequence_contrib\'] != \'\'</filter>\n+ </token>\n+ </expand>\n+ </outputs>\n+ <tests>\n+ <test expect_num_outputs="1">\n+ <param name="input" ftype="tabular" value="pred_metagenome_unstrat.tsv.gz"/>\n+ <param name="skip_minpath" value="true"/>\n+ <param name="no_gap_fill" value="true"/>\n+ <param name="no_regroup" value=""/>\n+ <conditional name="strat_output">\n+ <param name="per_sequence_contrib" value=""/>\n+ </conditional>\n+ <param name="intermediate_check" value="false"/>\n+ <output name="pathways_output" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="pathway"/>\n+ <has_n_lines n="205"/>\n+ </assert_contents>\n+ </output>\n+ <assert_command>\n+ \n+ <has_text text="--no_regroup" negate="true"/>\n+ <has_text text="--regroup_map" negate="true"/>\n+ </assert_command>\n+ </test>\n+ <test expect_num_outputs="6">\n+ <param name="input" ftype="tabular" value="pred_metagenome_unstrat.tsv.gz"/>\n+ <param name="skip_minpath" value="true"/>\n+ <param name="no_gap_fill" value="true"/>\n+ <param name="no_regroup" value=""/>\n+ <param name="intermediate_check" value="false"/>\n+ <conditional name="strat_output">\n+ <param name="per_sequence_contrib" value="--per_sequence_contrib"/>\n+ <param name="wide_table" value="false"/>\n+ <param name="per_sequence_abun" ftype="tabular" value="seqtab_norm.tsv.gz"/>\n+ <param name="per_sequence_function" ftype="tabular" value="per_seq_func.tsv.gz"/>\n+ </conditional>\n+ <p'..b' </assert_contents>\n+ </output>\n+ <output name="path_cov_unstrat" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="100CHE6KO"/>\n+ <has_n_lines n="92"/>\n+ </assert_contents>\n+ </output>\n+ <output name="path_abun_unstrat_per_seq" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="101CHE6WT"/>\n+ <has_n_lines n="3"/>\n+ </assert_contents>\n+ </output>\n+ <output name="path_abun_predictions" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="PWY-5837"/>\n+ <has_n_lines n="3"/>\n+ </assert_contents>\n+ </output>\n+ <output name="path_abun_contrib" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="taxon"/>\n+ <has_n_lines n="7"/>\n+ </assert_contents>\n+ </output>\n+ <output_collection name="pathways_intermediate_output" type="list" count="2">\n+ <element name="parsed_mapfile" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="METHYLENETHFDEHYDROG"/>\n+ <has_n_lines n="575"/>\n+ </assert_contents>\n+ </element>\n+ <element name="regrouped_infile" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="100CHE6KO"/>\n+ <has_n_lines n="1790"/>\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+@HELP_HEADER@\n+\n+Infer pathway abundances\n+========================\n+Infer the presence and abundances of pathways based on gene family abundances in a sample. By default, this script expects a table of E.C. number abundances (as output by PICRUSt2). However, alternative reaction to pathways mapping files can also be specified. By default, E.C. numbers are first regrouped to MetaCyc reactions, which are then linked to MetaCyc pathways through the default database.\n+\n+Pathway abundances are calculated using the same approach as HUMAnN2 based on the abundances of gene families that can be linked to reactions within pathways (E.C. numbers regrouped to MetaCyc reactions be default). By default, pathways will first be identified as present or not with MinPath.\n+\n+Either a structured or unstructured pathway mapfile can be input (the mapfile is structured by default), which will identify which set of pathways are likely present based on the presence of requisite gene families.\n+\n+Note\n+====\n+Stratified output will only be output if a stratified metagenome is input (or if --per_sequence_contrib is set). Please note that by default stratified abundances are based on how much predicted genomes (e.g. sequences) contribute to the community-wide abundance, not the abundance of the pathway based on the predicted genes in that genome alone. In other words, a predicted genome might be contributing greatly to the community-wide pathway abundance simply because one required gene for that pathway is at extremely high abundance in that genome even though no other required genes for that pathway are present. In contrast, the --per_sequence_contrib option should be used to get the predicted abundance and coverage of each pathway based on the predicted gene families within each genome. Note that using the --per_sequence_contrib option can greatly increase runtime.\n+\n+Input\n+=====\n+Input tabular table of gene family abundances (either the unstratified or stratified output of metagenome_pipeline.py).\n+\n+Output\n+======\n+Pathway abundance.\n+\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1038/s41587-020-0548-6</citation>\n+ </citations>\n+</tool>\n\\ No newline at end of file\n'

diff -r 000000000000 -r 6077821e8ae7 test-data/16S_predicted_and_nsti.tsv.gz

Binary file test-data/16S_predicted_and_nsti.tsv.gz has changed

diff -r 000000000000 -r 6077821e8ae7 test-data/EC_predicted.tsv.gz

Binary file test-data/EC_predicted.tsv.gz has changed

diff -r 000000000000 -r 6077821e8ae7 test-data/ec_unstrat_test.txt.gz

Binary file test-data/ec_unstrat_test.txt.gz has changed

diff -r 000000000000 -r 6077821e8ae7 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 6077821e8ae7 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 20:27:27 2023 +0000

[

b'@@ -0,0 +1,3680 @@\n+HMMER3/f [3.1b2 | February 2015]\n+NAME img_centroid_16S_aligned_head30\n+LENG 1219\n+MAXL 1483\n+ALPH DNA\n+RF no\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Wed Oct 10 17:19:17 2018\n+NSEQ 15\n+EFFN 1.680908\n+CKSUM 4036506208\n+STATS LOCAL MSV -13.3981 0.69577\n+STATS LOCAL VITERBI -14.9113 0.69577\n+STATS LOCAL FORWARD -6.1644 0.69577\n+HMM A C G T \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 1.37152 1.48531 1.23220 1.47755\n+ 1.26208 1.34388 1.26814 1.74440\n+ 0.30721 1.43238 3.65865 3.23874 0.04000 0.00000 *\n+ 1 0.35395 2.43840 2.24483 2.25526 43 a - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.14543 3.65865 2.21110 1.46634 0.26236 1.09861 0.40547\n+ 2 2.12949 2.47053 0.36672 2.26761 44 g - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.05789 3.57112 3.57112 1.46634 0.26236 1.83302 0.17427\n+ 3 1.87475 1.35652 1.96136 0.80211 45 t - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.05789 3.57112 3.57112 1.46634 0.26236 1.83302 0.17427\n+ 4 1.83494 2.02013 0.70400 1.54583 46 g - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.05789 3.57112 3.57112 1.46634 0.26236 0.38546 1.13987\n+ 5 2.26480 2.65592 0.30114 2.45412 47 g - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.05291 3.65865 3.65865 1.46634 0.26236 1.09861 0.40547\n+ 6 2.31076 0.40279 2.41667 1.94391 48 c - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.05291 3.65865 3.65865 1.46634 0.26236 1.09861 0.40547\n+ 7 2.26480 2.65592 0.30114 2.45412 49 g - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.05291 3.65865 3.65865 1.46634 0.26236 1.09861 0.40547\n+ 8 1.40350 1.84283 0.86745 1.73799 50 g - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.05291 3.65865 3.65865 1.46634 0.26236 1.09861 0.40547\n+ 9 0.35395 2.43840 2.24483 2.25526 51 a - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.05291 3.65865 3.65865 1.46634 0.26236 1.09861 0.40547\n+ 10 2.31076 0.40279 2.41667 1.94391 52 c - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.05291 3.65865 3.65865 1.46634 0.26236 1.09861 0.40547\n+ 11 2.26480 2.65592 0.30114 2.45412 53 g - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.05291 3.65865 3.65865 1.46634 0.26236 1.09861 0.40547\n+ 12 2.26480 2.65592 0.30114 2.45412 54 g - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.05291 3.65865 3.65865 1.46634 0.26236 1.09861 0.40547\n+ 13 2.26480 2.65592 0.30114 2.45412 55 g - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.05291 3.65865 3.65865 1.46634 0.26236 1.09861 0.40547\n+ 14 2.18399 2.01659 2.27039 0.42920 56 t - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.05291 3.65865 3.65865 1.46634 0.26236 1.09861 0.40547\n+ 15 2.26480 2.65592 0.30114 2.45412 57 g - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.05291 3.65865 3.65865 1.46634 0.26236 1.09861 0.40547\n+ 16 0.35395 2.43840 2.24483 2.25526 58 a - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.05291 3.65865 3.65865 1.46634 0.26236 1.09861 0.40547\n+ 17 2.26480 2.65592 0.30114 2.45412 59 g - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.05291 3.65865 3.65865 1.46634 0.26236 1.09861 0.40547\n+ 18 2.18399 2.01659 2.27039 0.42920 60 t - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.05291 3.65865 3.65865 1.46634 0.26236 1.09861 0.40547\n+ 19 0.35395 2.43840 2.24483 2.25526 61 a - - -\n+ 1.38629 1.38629 1.38629 1.'..b'1.46634 0.26236 2.34938 0.10029\n+ 1198 1.94221 2.21786 0.48684 2.01586 1245 g - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.06597 3.44458 3.44458 1.46634 0.26236 2.34938 0.10029\n+ 1199 1.94221 2.21786 0.48684 2.01586 1246 g - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.06597 3.44458 3.44458 1.46634 0.26236 2.34938 0.10029\n+ 1200 1.57314 1.71601 1.78160 0.81090 1247 t - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.06597 3.44458 3.44458 1.46634 0.26236 2.34938 0.10029\n+ 1201 1.59962 2.05950 0.67079 1.83756 1248 g - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.06597 3.44458 3.44458 1.46634 0.26236 2.34938 0.10029\n+ 1202 1.72062 1.85516 0.87773 1.39073 1249 g - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.06597 3.44458 3.44458 1.46634 0.26236 2.34938 0.10029\n+ 1203 1.94221 2.21786 0.48684 2.01586 1250 g - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.06597 3.44458 3.44458 1.46634 0.26236 2.34938 0.10029\n+ 1204 0.82758 1.92935 1.43817 1.71318 1251 a - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.06597 3.44458 3.44458 1.46634 0.26236 2.34938 0.10029\n+ 1205 1.77374 1.15390 1.83582 1.03447 1252 t - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.06597 3.44458 3.44458 1.46634 0.26236 2.34938 0.10029\n+ 1206 1.17100 1.55167 1.62536 1.26866 1253 a - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.06597 3.44458 3.44458 1.46634 0.26236 2.34938 0.10029\n+ 1207 1.35694 1.51038 1.19593 1.51730 1254 g - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.06597 3.44458 3.44458 1.46634 0.26236 2.34938 0.10029\n+ 1208 0.58838 2.05131 1.82480 1.86460 1255 a - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.06597 3.44458 3.44458 1.46634 0.26236 2.34938 0.10029\n+ 1209 1.88494 1.75948 1.92667 0.63413 1256 t - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.06597 3.44458 3.44458 1.46634 0.26236 2.34938 0.10029\n+ 1210 1.94221 2.21786 0.48684 2.01586 1257 g - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.06597 3.44458 3.44458 1.46634 0.26236 2.34938 0.10029\n+ 1211 0.58838 2.05131 1.82480 1.86460 1258 a - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.06597 3.44458 3.44458 1.46634 0.26236 2.34938 0.10029\n+ 1212 1.77113 1.21984 1.83225 0.98208 1259 t - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.06597 3.44458 3.44458 1.46634 0.26236 2.34938 0.10029\n+ 1213 1.88494 1.75948 1.92667 0.63413 1260 t - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.06597 3.44458 3.44458 1.46634 0.26236 2.34938 0.10029\n+ 1214 1.94221 2.21786 0.48684 2.01586 1261 g - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.06597 3.44458 3.44458 1.46634 0.26236 2.34938 0.10029\n+ 1215 1.94221 2.21786 0.48684 2.01586 1262 g - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.06597 3.44458 3.44458 1.46634 0.26236 2.34938 0.10029\n+ 1216 1.94221 2.21786 0.48684 2.01586 1263 g - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.06597 3.44458 3.44458 1.46634 0.26236 2.34938 0.10029\n+ 1217 1.94221 2.21786 0.48684 2.01586 1264 g - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.06597 3.44458 3.44458 1.46634 0.26236 2.34938 0.10029\n+ 1218 1.88494 1.75948 1.92667 0.63413 1265 t - - -\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.06597 3.44458 3.44458 1.46634 0.26236 2.34938 0.10029\n+ 1219 1.94221 2.21786 0.48684 2.01586 1266 g - - -\n+ 1.09892 1.67037 1.28581 1.59867\n+ 0.35693 1.20338 * 2.84032 0.06018 0.00000 *\n+//\n'

diff -r 000000000000 -r 6077821e8ae7 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 20:27:27 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 6077821e8ae7 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 20:27:27 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 6077821e8ae7 test-data/known_traits.tsv.gz

Binary file test-data/known_traits.tsv.gz has changed

diff -r 000000000000 -r 6077821e8ae7 test-data/metadata.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/metadata.tsv Sat Mar 04 20:27:27 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 6077821e8ae7 test-data/out_tree.zip

Binary file test-data/out_tree.zip has changed

diff -r 000000000000 -r 6077821e8ae7 test-data/per_seq_func.tsv.gz

Binary file test-data/per_seq_func.tsv.gz has changed

diff -r 000000000000 -r 6077821e8ae7 test-data/pred_metagenome_strat.tsv.gz

Binary file test-data/pred_metagenome_strat.tsv.gz has changed

diff -r 000000000000 -r 6077821e8ae7 test-data/pred_metagenome_unstrat.tsv.gz

Binary file test-data/pred_metagenome_unstrat.tsv.gz has changed

diff -r 000000000000 -r 6077821e8ae7 test-data/seqtab_norm.tsv.gz

Binary file test-data/seqtab_norm.tsv.gz has changed

diff -r 000000000000 -r 6077821e8ae7 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 20:27:27 2023 +0000

@@ -0,0 +1,10 @@
+>02905cfb87861c837dde629596d9272b
+TGGTCTTGACATCCCTCTGACGAGTGAGTAATGTCGCTTTCCCTTCGGGGCAGAGGAGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATCTTTAGTAGCCAGCAGTAAGATGGGAACTCTAGAGAGACTGCCGGGGATAACCCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCCTTATGACCAGGGCTACACACGTGCTACAATGGCGTAAACAGAGGGAAGCGACCCTGTGAAGGTAAGCAAATCCCAAAAATAACGTCTCAGTTCGGATTGTAGTCTGCAACTCGACTACATGAAGCTGGAATCGCTAGTAATCGCGAATCAGAATGTCGCGGTGAATACGTTCCCGG
+>03562a221b15ef37470e4567e112f35f
+CGGGCTTGAAAGTTAGTGACCGGAGATGAAAGTCTCCTTTCTATAGCAATATAGACACGAAACTAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCTTTTCTTCAGTTACCATCATTAAGTTGGGGACTCTGAAGACACTGCCATCGTAAGATGTGAGGAAGGATGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCGACACACGTGTTACAATGGCGTGGACAGCGGGGAACGAGGTGGCGACACCGAGGGAATCCCGAAACCACGTCCCAGTTCGGATTGGAGTCTGCAACTCGACTCCATGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCATGGCGCGGTGAATACGTTC
+>03af6a6644bc358ee6716cbb44a5a479
+AGGGCTTGACATATATCAGAATATACTAGAGATAGTATAGTCCTTCGGGACTGATATACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTGTCCTTAGTTGCCAGCACGTAAAGGTGGGAACTCTAAGGAGACTGCCGGTGATAAATCGGAGGAAGGTGGGGATGACGTCAAATCATCATGCCCTTTATGTCCTGGGCTACACACGTACTACAATGGCCGTGACAGAGAGAAACGAAACAGTGATGTGGAGTAAAACTCTAAAAGCGGTCTCAGTTCGGATTGAAGGCTGAAATTCGCCTTCATGAAGCTGGAATTGCTAGTAATGGCAGGTCAGCATACTGCCGTGAATACGTTCCCGG
+>03cb13abd3f1c5444360e489460bdfb0
+CGGGCTCAAACGGAAGGGGACGGATTGTGAAAGCAGTCTTTCCTTCGGGACCGCTTCCGAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCCTACCGACAGTTGCTAACAGATTAAGCTGAGGACTCTGTCGGGACTGCCGGCGCAAGCTGTGAGGAAGGCGGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCGACACACGTGTTACAATGGCAGGTACAGCGGGAAGCCACCCGGCGACGGGGCGCGGAACCCGAAAACCTGTCTCAGTTCGGATTGGAGTCTGCAACCCGACTCCATGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCACGGCGCGGTGAATACGTTCCCG
+>05f9281835817fddd06162cd69497a2d
+CGGGCTTAAATTGCATCTGAATGATTTGGAAACAGATCAGCCGCAAGGCAGATGTGAAGGTGCTGCATGGTTGTCGTCAGCTCGTGCCGTGAGGTGTCGGCTTAAGTGCCATAACGAGCGCAACCCTTGCTGTCAGTTACTAACAGGTCATGCTGAGGACTCTGACGGGACTGCCATCGTAAGATGTGAGGAAGGTGGGGATGACGTCAAATCAGCACGGCCCTTACGTCCGGGGCTACACACGTGTTACAATGGGGGGTACAGCAGGCAGCTACCTGGCGACAGGATGCTAATCCCGAAAGCCCCTCTCAGTTCGGATTGGAGTCTGCAACCCGACTCCATGAAGCTGGATTCGCTAGTAATCGCGCATCAGCCACGGCGCGGTGAATACGTTCCCGGG

diff -r 000000000000 -r 6077821e8ae7 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 20:27:27 2023 +0000

diff -r 000000000000 -r 6077821e8ae7 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 20:27:27 2023 +0000

diff -r 000000000000 -r 6077821e8ae7 test-data/table.biom

Binary file test-data/table.biom has changed

diff -r 000000000000 -r 6077821e8ae7 test-data/table.mothur.shared
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/table.mothur.shared Sat Mar 04 20:27:27 2023 +0000

@@ -0,0 +1,25 @@
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+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
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+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

diff -r 000000000000 -r 6077821e8ae7 test-data/weighted_nsti.tsv.gz

Binary file test-data/weighted_nsti.tsv.gz has changed

diff -r 000000000000 -r 6077821e8ae7 test-data/workflow_seq_abun.biom

Binary file test-data/workflow_seq_abun.biom has changed