Galaxy |

Changeset 0:078414a1226b (2022-10-14)

Next changeset 1:5ae13a156271 (2023-03-27)

Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"

added:
generate_cannot_links.xml
macros.xml
test-data/S1.fasta
test-data/S10.fasta
test-data/S2.fasta
test-data/S3.fasta
test-data/S4.fasta
test-data/S5.fasta
test-data/S6.fasta
test-data/S7.fasta
test-data/S8.fasta
test-data/S9.fasta
test-data/cannot.txt
test-data/data.csv
test-data/data_split.csv
test-data/input_coassembly_sorted1.bam
test-data/input_coassembly_sorted2.bam
test-data/input_coassembly_sorted3.bam
test-data/input_coassembly_sorted4.bam
test-data/input_coassembly_sorted5.bam
test-data/input_multi.fasta.gz
test-data/input_multi_sorted1.bam
test-data/input_multi_sorted10.bam
test-data/input_multi_sorted2.bam
test-data/input_multi_sorted3.bam
test-data/input_multi_sorted4.bam
test-data/input_multi_sorted5.bam
test-data/input_multi_sorted6.bam
test-data/input_multi_sorted7.bam
test-data/input_multi_sorted8.bam
test-data/input_multi_sorted9.bam
test-data/input_single.bam
test-data/input_single.fasta
test-data/input_single_2.fasta
test-data/input_single_3.fasta
test-data/model.h5
test-data/taxonomy.tsv
test-data/taxonomy_10.tsv
test-data/taxonomy_2.tsv
test-data/taxonomy_3.tsv
test-data/taxonomy_4.tsv
test-data/taxonomy_5.tsv
test-data/taxonomy_6.tsv
test-data/taxonomy_7.tsv
test-data/taxonomy_8.tsv
test-data/taxonomy_9.tsv
test-data/test-db/GTDB
test-data/test-db/GTDB.dbtype
test-data/test-db/GTDB.index
test-data/test-db/GTDB_mapping
test-data/test-db/GTDB_merged.dmp
test-data/test-db/GTDB_names.dmp
test-data/test-db/GTDB_nodes.dmp
test-data/test_database.loc
tool-data/gtdb.loc.sample
tool_data_table_conf.xml.sample
tool_data_table_conf.xml.test

diff -r 000000000000 -r 078414a1226b generate_cannot_links.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/generate_cannot_links.xml Fri Oct 14 21:35:24 2022 +0000

[

@@ -0,0 +1,138 @@
+<tool id="semibin_generate_cannot_links" name="SemiBin: Contig annotations"  version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>
+
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <expand macro="version"/>
+    <command detect_errors="exit_code"><![CDATA[
+#import re
+@FASTA_FILES@
+SemiBin
+    generate_cannot_links
+    --input-fasta 'contigs.fasta'
+    --output 'output'
+    --cannot-name 'cannot'
+#if $mode.ref.select == "cached"
+    --reference-db-data-dir '$mode.ref.cached_db.fields.path'
+#else
+    --taxonomy-annotation-table '$mode.ref.taxonomy_annotation_table'
+#end if
+    @MIN_LEN@
+#if str($ml_threshold) != ''
+    --ml-threshold $ml_threshold
+#end if
+    --cannot-name 'cannot'
+    --threads \${GALAXY_SLOTS:-1}
+    --processes \${GALAXY_SLOTS:-1}
+    ]]></command>
+    <inputs>
+        <conditional name="mode">
+            <expand macro="mode_select"/>
+            <when value="single">
+                <expand macro="input-fasta-single"/>
+                <expand macro="ref-single"/>
+            </when>
+            <when value="co">
+                <expand macro="input-fasta-single"/>
+                <expand macro="ref-single"/>
+            </when>
+            <when value="multi">
+                <expand macro="input-fasta-multi"/>
+                <expand macro="ref-multi"/>
+            </when>
+        </conditional>
+        <expand macro="min_len"/>
+        <expand macro="ml-threshold"/>
+    </inputs>
+    <outputs>
+        <expand macro="cannot_link_output"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <conditional name="mode">
+                <param name="select" value="single"/>
+                <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
+                <conditional name="ref">
+                    <param name="select" value="taxonomy"/>
+                    <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
+                </conditional>
+            </conditional>
+            <conditional name="min_len">
+                <param name="method" value="min-len"/>
+                <param name="min_len" value="0" />
+            </conditional>
+            <param name="ml_threshold" value=""/>
+            <output name="cannot" ftype="txt">
+                <assert_contents>
+                    <has_text text="g1k_0,g4k_0"/>
+                    <has_text text="g2k_3,g4k_5"/>
+                    <has_text text="g4k_6,g4k_5"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="mode">
+                <param name="select" value="single"/>
+                <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
+                <conditional name="ref">
+                    <param name="select" value="taxonomy"/>
+                    <param name="taxonomy_annotation_table" value="taxonomy.tsv"/>
+                </conditional>
+            </conditional>
+            <conditional name="min_len">
+                <param name="method" value="min-len"/>
+                <param name="min_len" value="0" />
+            </conditional>
+            <param name="ml_threshold" value=""/>
+            <output name="cannot" ftype="txt">
+                <assert_contents>
+                    <has_text text="g1k_0,g4k_0"/>
+                    <has_text text="g2k_3,g4k_5"/>
+                    <has_text text="g4k_6,g4k_5"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <conditional name="mode">
+                <param name="select" value="single"/>
+                <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
+                <conditional name="ref">
+                    <param name="db_selector" value="cached"/>
+                    <param name="cached_db" value="test-db"/>
+                </conditional>
+            </conditional>
+            <conditional name="min_len">
+                <param name="method" value="min-len"/>
+                <param name="min_len" value="0" />
+            </conditional>
+            <param name="ml_threshold" value=""/>
+            <output name="cannot" ftype="txt">
+                <assert_contents>
+                    <has_text text="g1k_0,g2k_0"/>
+                    <has_text text="g2k_9,g4k_1"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+@HELP_HEADER@
+
+This tool runs the contig annotations using mmseqs with GTDB and generate cannot-link file used in the semi-supervised deep learning model training.
+
+Inputs
+======
+
+@HELP_INPUT_FASTA@
+
+Outputs
+=======
+
+@HELP_CANNOT@
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>

diff -r 000000000000 -r 078414a1226b macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Fri Oct 14 21:35:24 2022 +0000

[

b'@@ -0,0 +1,351 @@\n+<?xml version="1.0"?>\n+<macros>\n+ <token name="@TOOL_VERSION@">1.1.1</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@PROFILE@">21.01</token>\n+ <xml name="biotools">\n+ <xrefs>\n+ <xref type="bio.tools">semibin</xref>\n+ </xrefs>\n+ </xml>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">semibin</requirement>\n+ <yield/>\n+ </requirements>\n+ </xml>\n+ <xml name="version">\n+ <version_command>SemiBin -v</version_command>\n+ </xml>\n+ <xml name="mode_fasta_bam">\n+ <conditional name="mode">\n+ <expand macro="mode_select"/>\n+ <when value="single">\n+ <expand macro="input-fasta-single"/>\n+ <expand macro="input-bam-single"/>\n+ </when>\n+ <when value="co">\n+ <expand macro="input-fasta-single"/>\n+ <expand macro="input-bam-multi"/>\n+ </when>\n+ <when value="multi">\n+ <expand macro="input-fasta-multi"/>\n+ <expand macro="input-bam-multi"/>\n+ </when>\n+ </conditional>\n+ </xml>\n+ <xml name="mode_fasta">\n+ <conditional name="mode">\n+ <expand macro="mode_select"/>\n+ <when value="single">\n+ <expand macro="input-fasta-single"/>\n+ </when>\n+ <when value="co">\n+ <expand macro="input-fasta-single"/>\n+ </when>\n+ <when value="multi">\n+ <expand macro="input-fasta-multi"/>\n+ </when>\n+ </conditional>\n+ </xml>\n+ <xml name="mode_select">\n+ <param name="select" type="select" label="Binning mode">\n+ <option value="single" selected="true">Single sample binning (each sample is assembled and binned independently)</option>\n+ <option value="co">Co-assembly binning (samples are co-assembled together and binned together)</option>\n+ <option value="multi">Multi-sample binning (multiple samples are assembled and binned individually, but information from multiple samples is used together)</option>\n+ </param>\n+ </xml>\n+ <xml name="input-fasta-single">\n+ <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="Contig sequences"/>\n+ </xml>\n+ <xml name="input-fasta-multi">\n+ <conditional name="multi_fasta">\n+ <param name="select" type="select" label="Contig files of the samples">\n+ <option value="concatenated" selected="true">1 concatenated file (created using the dedicated tool) with all sample contigs </option>\n+ <option value="multi">1 contig file per sample</option>\n+ </param>\n+ <when value="concatenated">\n+ <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="Combined contig sequences"/>\n+ <expand macro="separator"/>\n+ </when>\n+ <when value="multi">\n+ <param argument="--input-fasta" type="data" multiple="true" format="fasta,fasta.gz" label="Contig sequences"/>\n+ <expand macro="concat_min_len"/>\n+ </when>\n+ </conditional>\n+ </xml>\n+ <xml name="concat_min_len">\n+ <param name="min_len" type="integer" min="0" value="0" label="Minimal length for contigs to be kept"/>\n+ </xml>\n+ <token name="@SINGLE_FASTA_FILES@"><![CDATA[\n+#if $input_fasta.ext.endswith(".gz")\n+gunzip -c \'$input_fasta\' > \'contigs.fasta\' &&\n+#else\n+ln -s \'$input_fasta\' \'contigs.fasta\' &&\n+#end if\n+ ]]></token>\n+ <token name="@FASTA_FILES@"><![CDATA[\n+#if $mode.select == \'single\' or $mode.select == \'co\'\n+ #if $mode.input_fasta.ext.endswith(".gz")\n+gunzip -c \'$mode.input_fasta\' > \'contigs.fasta\' &&\n+ #else\n+ln -s \'$mode.input_fasta\' \'contigs.fasta\' &&\n+ #end if\n+#else\n+ #if $mode.multi_fasta.select == \'concate'..b'${on_string}: Coverage">\n+ <filter>mode["select"]=="co" and extra_output and "coverage" in extra_output</filter>\n+ <discover_datasets pattern=".*\\.bam_(?P<designation>.*)_data_cov\\.csv" format="csv" directory="output/" />\n+ </collection>\n+ <collection name="co_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample">\n+ <filter>mode["select"]=="co" and extra_output and "coverage" in extra_output</filter>\n+ <discover_datasets pattern=".*\\.bam_(?P<designation>.*)_data_split_cov\\.csv" format="csv" directory="output/" />\n+ </collection>\n+ <collection name="multi_cov" type="list" label="${tool.name} on ${on_string}: Coverage">\n+ <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter>\n+ <discover_datasets pattern=".*\\.bam_(?P<designation>.*)_data_cov.csv" format="csv" directory="output/samples/" />\n+ </collection>\n+ <collection name="multi_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage per sample">\n+ <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter>\n+ <discover_datasets pattern="(?P<designation>.*)\\/data_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>\n+ </collection>\n+ <collection name="multi_split_cov" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample">\n+ <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter>\n+ <discover_datasets pattern=".*\\.bam_(?P<designation>.*)_data_split_cov.csv" format="csv" directory="output/samples/" />\n+ </collection>\n+ <collection name="multi_split_cov_sample" type="list" label="${tool.name} on ${on_string}: Coverage (split data) per sample">\n+ <filter>mode["select"]=="multi" and extra_output and "coverage" in extra_output</filter>\n+ <discover_datasets pattern="(?P<designation>.*)\\/data_split_cov.csv" format="csv" directory="output/samples/" recurse="true" match_relative_path="true"/>\n+ </collection>\n+ <collection name="multi_contigs" type="list" label="${tool.name} on ${on_string}: Contigs">\n+ <filter>mode["select"]=="multi" and extra_output and "contigs" in extra_output</filter>\n+ <discover_datasets pattern="(?P<designation>.*).fa" format="fasta" directory="output/samples/" />\n+ </collection>\n+ </xml>\n+ <xml name="train_output">\n+ <data name="model" format="h5" from_work_dir="output/model.h5" label="${tool.name} on ${on_string}: Semi-supervised deep learning model" />\n+ </xml>\n+ <xml name="cannot_link_output">\n+ <data name="cannot" format="txt" from_work_dir="output/cannot/cannot.txt" label="${tool.name} on ${on_string}: Cannot-link constraints" />\n+ </xml>\n+ <token name="@HELP_HEADER@"><![CDATA[\n+What it does\n+============\n+\n+SemiBin is a Semi-supervised siamese neural network for metagenomic binning\n+\n+]]></token>\n+ <token name="@HELP_INPUT_FASTA@"><![CDATA[\n+- Contigs in fasta for 1 or several samples from single or co-assembly\n+]]></token>\n+ <token name="@HELP_INPUT_BAM@"><![CDATA[\n+- BAM with reads mapping to the contigs\n+]]></token>\n+ <token name="@HELP_CANNOT@"><![CDATA[\n+- Cannot-link constraints\n+]]></token>\n+ <token name="@HELP_DATA@"><![CDATA[\n+- Training data and split training data for the model\n+]]></token>\n+ <token name="@HELP_MODEL@"><![CDATA[\n+- Semi-supervised deep learning model\n+]]></token>\n+ <token name="@HELP_BINS@"><![CDATA[\n+- Reconstructed bins after reclustering\n+- Reconstructed bins before reclustering\n+]]></token>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1038/s41467-022-29843-y</citation>\n+ </citations>\n+ </xml>\n+</macros>\n\\ No newline at end of file\n'

diff -r 000000000000 -r 078414a1226b test-data/S1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/S1.fasta Fri Oct 14 21:35:24 2022 +0000

b'@@ -0,0 +1,13400 @@\n+>g1k_0\n+ATGGCTAATAATTATCAAACTTTATATGATTCAGCAATAAAAAGGATTCCATACGATCTT\n+ATTTCTGATCAAGCTTATGCAATTCTACAAAATGCTAAAACTCATAAAGTTTGCGATGGT\n+GTTTTATATATAATTGTAGCCAATGCCTTTGAAAAAAGTATTATTAACGGTAATTTTATT\n+AACATTATTTCTAAATATCTAAGCGAAGAATTCAAAAAGGAAAATATTGTTAATTTTGAA\n+TTTATTATAGACAATGAAAAATTATTAATTAATAGCAATTTTTTAATTAAAGAAACTAAT\n+ATTAAAAATCGTTTTAATTTTAGTGATGAACTTTTACGTTACAATTTTAACAATTTAGTA\n+ATTAGTAATTTTAATCAAAAAGCGATTAAGGCGATTGAAAATTTATTTTCAAATAACTAT\n+GATAATAGTTCAATGTGTAACCCTTTATTTTTATTTGGTAAAGTTGGTGTTGGTAAAACG\n+CATATCGTGGCTGCTGCTGGTAATCGTTTTGCTAATAGTAATCCTAATTTAAAAATTTAT\n+TATTATGAAGGGCAAGATTTTTTTCGAAAGTTTTGTTCTGCTTCGTTAAAAGGGACTAGT\n+TATGTTGAAGAGTTTAAAAAAGAAATTGCTTCAGCAGATTTATTAATTTTTGAAGATATT\n+CAAAATATCCAATCACGTGATTCAACGGCTGAATTGTTTTTTAATATCTTTAATGATATA\n+AAATTAAATGGTGGAAAAATTATCTTAACATCTGACCGTACACCAAACGAACTTAATGGT\n+TTTCATAATCGAATTATTTCGAGATTAGCGTCAGGTTTGCAGTGTAAAATTTCTCAACCC\n+GACAAAAATGAAGCTATTAAAATTATTAATAATTGGTTTGAATTCAAAAAAAAATATCAA\n+ATTACTGACGAAGCTAAAGAATATATTGCTGAAGGTTTTCACACTGATATTAGACAGATG\n+ATTGGTAATCTAAAACAAATTTGTTTTTGAGCGGACAATGATACTAATAAAGATTTAATA\n+ATCACAAAAGATTATGTAATTGAGTGTTCAGTTGAAAACGAAATTCCACTAAATATTGTT\n+GTTAAAAAACAATTTAAACCTGAACAAATAATTGAAATTGTTGCAAAAGAATTAAATATA\n+AAAACAGATTTAATTAAATCTTCTATTAGAAAAAATAATATAGTTTGAGCGCGTGATATT\n+GTTTGTTATATTCTAAAAAATAAACTAAATTTAACTTTAACAGATATTGGTAAATTACTA\n+AACGGACGAGAACACACTACAATTAGTCATAGTATTAGTAAAGTTCAAAAAATTCTTGAT\n+GATGAAAATAGTCAAGAAGCACTACAAATTAATCTAATTATCAATAAATTTTAATTTTAT\n+TAAAGAAAAGTAATCAAAACTTATTAAAATATTATATATTTATATATAGTGTATTTTCGT\n+GTTTTTGAACTCAAAACATAAAATTACTAATTTTTTATTATTTAACTTATATATTGTAAT\n+AAAGGAAGAGAATTATGAGAGATATTCATCCAGTAAGCAAACCATGCGTTTATAATTGTG\n+TAACATGTAAAAAAGAATTTATAATTGATTCTGCAGCAAAAAATACAGAAGTTGCAATTG\n+AAGTTTGTTCAAATTGCCATACATTTTTTATTGGTAAACAAAACGCAACTACAACATTAC\n+GTGGTCGTGCTGAAAAACTAAATAATCGTTTTGAAGCTGGTTTAAATAACATTAATAAAA\n+AACCAGAAAAGAAAAAAATACAAGGTAAATCTGAACCAAGAAAAAGTTTAAACGAATTAT\n+AATTAATCATCTTGTCATTAATTGCCAAGATTGTTTAATTCTTTTTGTATAATTAAAAAT\n+TAGTAGATTAAATAACAGGCAATTAGATTACCTGTTATTTTATTTTTACTAAAATATTTA\n+AAACTGAGGGACTTATGGAATACAACAAAAAACTTTATGAAGCAATTGAACGAGTCGCTA\n+TTAAAAATGACGCTTTAAAAAAAGAATTAGAAACGGTTGTAACAGACTTTAAAAAAATTA\n+AAGAGATTAATATACAGTTAAAAAAAACTACTAAAATTGCTGAAGCCTTTGCAAAATATA\n+AACAAAAATTGGATACTGGTATAGCTGCTGAAAAAATATTAAATACAGAAAAAGATTTAG\n+AATTAATCGAATTAGCACAGATGGATTTAGATGAAGCTAAAATTAATATTCCAATAATTG\n+AAAATGATTTAAAAATTATGCTGTTGCCAACTGATCCTAATGATGATAAAAATGTTATTG\n+TTGAAATGCGCCCTGCTGCTGGAGGGGATGAATCATCAATTTTTGTCGGCAATTTGTTTG\n+ATACATATCGTGCTTATGCTGAAAATAATAATTGAAAAATGAAAATTATAGAAATGACTC\n+CGAATGCTGTTGGTTTTAGTTTTATTTCTTTTATGATTTCTGGAGAAGAAGTTTATTCAC\n+GAATGAAATTTGAGTCAGGAGTTCATCGAGTACAACGTGTACCTGCTACTGAATCTAAAG\n+GAAGAGTACATACGTCAACAATTACAGTTGCTGTTCTTCCAGAACAAGATGAAGTTGATG\n+TTGTAATTAATCCAACAGAATTAAGAATTGATACTTACCGTGCAAGTGGGGCTGGAGGAC\n+AGCATGTTAATAGAACAGAATCAGCTGTAAGAATTACGCATATTCCAACAGGGGTTGTTG\n+CTGCATGTCAAGAGGGAAAATCACAAATTGAAAACCGAGAAACAGCTATGAAAATGTTAA\n+GAGCTAAATTATGAGAAGCAGCTCAAGAACAGCAAAATGCAGAATTTGCTAATTTAAGAA\n+AAAATCAAGTTGGTACAGGGGATCGTTCTGAAAAAATCCGTACTTACAATTATCCACAGA\n+ACCGCGTTACTGACCATCGTATTAACCTAACATTAAATAAATTAGACCAAATCATGATGG\n+GTGAGTTAGATGAGATTATTGATGCATTAATTGCTGACGAACAAACTGGTTTAATGGCTA\n+ATTTAGATATTTAATGACCTACCATCAATTAATTTTTCAAGCATACTCACTACTTGAAAA\n+AAAATTACGTAATCCACAAGTAGCATTTCAGTTGCTGTACGGATTAGATAATAAAATTAA\n+CGATTCTTATAGTTTTTCAAATAACCGCTTAACAATTGTAAATTCTAATTTAGAATATAC\n+ATATTTTAAACTATTAGATGAATTTATTAATGGAAAACCATTAGTGAGAATTTTAGGATA\n+TGGCTATTTTTGTGCAAAGCGCTTTTATGTTGATAAAAATGTTTTTGCTTTTCGTGTTGA\n+AACTGAATTATTAATAGATGTTGTTAATAAAGTAATTCAACAATCCACTTATAAAATTAA\n+AAATGTTATTGATGTTTGTTGTGGTAGTGGTGTTTTAGGGTTAAGTACAAAAATGAATTT\n+TAATCAATTGAATGTTTCATTATTAGATATTTCTATTGATGCAATTAATAATTGCAAAAA\n+AAATGCTAAATATCATAACTTAACAGATGTAAATTTTATTCATAAAAGTATGCAAGAATA\n+CTTTTTAAACACAAAAAAACGGTTTGATTTAATTATCTGTAATCCCCCATATATCAAAAG\n+TAATTATGAATTAAATCGTGAAGTCTTAGATTATGACCCCATTAATGCACTTATTGATTT\n+CGATCACAAAGATGGAATTAGTTTTTATTTATTTATAATAAATAACATTAAATCAATTGC\n+TAATGAGAAATTCACTATTATTTTTGAAATTGGTTTTGATCAAAAAGAAATTTTAGAAAA\n+AGTTATTAAAAAAAATGAATTTCCTCTTTTTTACTACTTTATAAATGATTATAATAATCT\n+AT'..b'TTTATTTT\n+TTTCACTATCTTTTAAAACTCATCCATCGCTTGTTTTTGTAGCAAGATCTTCTAATTTTG\n+TAGTTCCTTTTGTTGAAAGAAGTTTAAATAATTCTTCATTTTGAATAACATTAACAATTT\n+GAGCATATGTAATTGCTTTTAAACCAGCTAGTTTAGCCGCTTGTTCTAAATAAACACGAC\n+CTGCATTTGATAATTCAACAAGCGGAGTATCATCTACATATGTGCTCTTATCTAAACTTG\n+CTTCAGTATGTGTTCCTAATTTATAAGCATCTTTATTAATATCATTAGTTAGTTGTGCAC\n+CTTTTGAAGCATTTTCAATTGCTCCCTTCATTGCTAAATCAACACGTTTAACAATTGAGA\n+ATAAAATTGTTTTTCCATCATTAACAGTTTTGTTTGTAATTCTTTTACGGTTTGTTACAT\n+CATCTAATTCTTGTGCAGTATCAACACCAATAATTACACTTGGATCTGTTGCATTTGAAA\n+CAATTGAAGTTGCAAGGTTTGTTTGTGGACCAGCTACAGGTAAAATAACATCAGCTTTTT\n+TTGTAATTAAATCATTGATAATGTTTGTTGCACCTTCTTCATCTGGTTTAAATGAACCAG\n+CAACGTATTTGCTAGCAAATACTTGTTCAACATTCATTCATTTTTTCTTGCTTCCATTAG\n+CATCTTCTTGATTAATTTCTTTATCTTTTAACTTTTCATTTGCTCATTGAACACCTAATT\n+TAAAACCTTGGATAAAAGTTGAAGTTGATGTAAAATGTAATCCAACATATCCACCTCAAG\n+TTAGTTTTCCATCTGCTGCAAAAGTTTTTTGGTTAGCATTTAAATAGTACGCCGCAGCAA\n+TACCTGTTAAAAATGCTGCTTGATCTACACGATATGAGACAGACGCAATACGGTCTTTAC\n+CCACTGTTCCACTAAATTTATCATCAATTAAAACTGCACTTAAATCTTTTTTATCGCTGC\n+TTGAACCAAAATATTCTTTAATTGGAATTGAGTGACTAAATGAAATCAAGCCTAACATAC\n+GAGCACCATCATCGTATAATGAATTATATGTTCTGTGATATCCTAAACTATCATCTCCAG\n+CTGGTTTTGCATAAAAATCTTCTAAAGACAATTTAGAAATATAATTTCCATCTTTATTTG\n+TTTTCCCATCATCTTTATTACTATCATTACATGATGCAGCAATAGCTGCAACTGAAGTTA\n+ATGTAACCACTCCAGCAAGTGATGCAAACAAGATTTTTTTATTGATTTTGCTTTTTTTCA\n+TAAAATTTATTTTTTATCCTTTTTGACATGAAAAATCTAAAATAACTAAACAACACAATT\n+TTTAAGATTGTGTAGTATCATTATACAAAAAATAAACTTGTATATATAAGTTAAACACTT\n+AATTTTTGTTTTTTGTATAAAAAAAAGCGTTTTTTTAATTAAAACACTTTTTTATTTTTT\n+AAAATTTAGAATTCTTAATGAATTTTCTAATAAGATTTTTTGCATTTTTTCATGTGTAAT\n+GCCTAATAAGTTGGCAATAAATGCTGATGTATATAATACATAATAAGGATAGTTAGTTTG\n+CCCTCGTTTAGGAACTGGTGTTAAATATGGGGCGTCTGTTTCTACTAGAATCTTATCAAG\n+TGGGGTTATTTTAATCGCCTCATACAGTTCATGTAATTGATTATTTTTTGTTGGTTTAAA\n+AGTAATTACACCAGGATATGAAATATAATAACCCATTTCAATATATTGTTGTGCATACTC\n+TTTTTTATCTGTAAAACAATGGATTATTACATCTTGAACAGCTAATTCTTTTAAGATGGC\n+AATTGCGTCATCGTGTGCATTACGGATGTGTAACATTAATGGTTTATGATACTTTTTAGC\n+CAATTCAATATGTTTTTTAAACCAATGTTTTTGAAAATCATGATCATAATTTTGTTCATG\n+ATAATAGTCTAAACCACACTCACCAATACAACTTATGTAATCAATATTTTCTGCTATCAA\n+TTTTTCTAATGCAACAAAATCATTTTCTATATTATGTAAATCATTAGGATGGATTGCAAC\n+ACTACAAGTCAAAAATTTAAATTTTTTAGCTTGTTGAATGGCTGTCTGTGAAGTTTTTAA\n+ATCTACTCCAACAATATTTAATCCAATACCTTGTTCATAACATTTAAAGATAATGTCATC\n+AAATTCTTCAATTAATGGTTCAATATTAGGATGAGTATGAGTATCAATAATTTTTATTTT\n+TTCTAACATATTATTTACCTATACAAAAATTTTTAAATAAATCATCTAAAAAATCATATT\n+CGCTACTTATGCCTAAGAGTTCATTTAAACGTAAATTGCAAAATTCTAAATCAGCGACAA\n+TTAAATCAAGTGTATCCCCTTTTTCTAAATTAAGAATTGCGTTATTAATTAAATAATGAA\n+CATTTTCTAAAATACCAATTTGACGTTGGGATTGTAAAACATCAATGTTAGCATTGTCAA\n+ACTCTTGAACATAAAAAAGTTTTTTAATTTCATCAATCAATGACTGAATATCATTATTTT\n+TTGCATTAATATATATTTGTTTATCATCGTATTGATCAACTAAATCTTTTTTTGTATAAA\n+CTAATAAATGTTTTTGTTTTTTAATTAAATCATATAACTCCAAATCTTGTTGTTCGTTTG\n+CAGGTATTAAATATAAAATTAAATCAACTTTATCAATTAATGCTTTGGCTTTATTAATTC\n+CTAAATTTTCAACAAAATCATTTGTTAAATGAATTCCTGCAGTATCTAAGATATTTAAAG\n+TAATATTATCAATATTAATTGAGGATTCAATAACATCACGTGTTGTCCCAGGAATATCTG\n+TAACAATCGCTTTTTGTTCATTGCATAAAGCGTTTAATAGAGTTGATTTACCTACATTTG\n+GTTTTCCAATTATTAACACCCTAATGCCTTTATTGATTGGTAAAAATTTTTTTGATTGAT\n+CAATAATTTTTGTAATTTTTTTATCTAAAGATAATAAACGTTGTTTTAAAATAATAGCAT\n+CAACTTGTTCAACATCATCGTATTCAGGATAATCAATATTAACTTCAATTTGCCCAATTA\n+TCATAAATAACTCATGCCTAAATTCAGCAATTGATTGCGAAACACGTCCTAATAGAGCGC\n+CAATTACACCTTTAACGCTTAATTCATTTTTAGCATTAACCAAATTGTTAATTGCTTCAA\n+TTTTTGATAAATCCATTTTTTTATTTAATAAAGCACGGCGAGAAAATTCTCCACGTTGTG\n+CTGGTTGACAACCATATTTAATTAATGTTTTAATAATTAAATTAGCAACCACTATTCCTC\n+CGTGGCAATTAATTTCTACTAAATCTTCTCCAGTAAATGTTTTTGGAGCTACAAATGTAT\n+TTATTAAAACTTCATCTAAAATTTGATTATCATCTTTTAGAATTGTATACCAAATTTTAA\n+AAGTTTCTTTTTTTATTTTTATTGTTGAAATTTTATTAATTATTTCAAAAGCTTTTGGAC\n+CACTAACCCGAATAATGTGAATGGCACAATTCATAGGCGCGGTTGCTAAAGCAACAATTG\n+TTGACATTGTTAATCACCTTTATTTTTATTAATAATTGTATAAATAATAGTAAACAAATT\n+ATTTTTATTAATATTAATTTTTAAATTCGCACGCATTAAATCCAAAATAATTTCTTTGCT\n+ATTTACATTATTAATTCTAATGAAGATTAATTTTAATAGATAATGAATTTGTAAGGTAGA\n+TAAATTTTTAAATATTTCTTTTAAATCATTTAATATTTCAAAACTTCTTAAATCACTTAA\n+TTTTCCATAATAAGTTAAAACATCATTGATTTCCTTGTTTTCTAATAAAATTTTTAGCTC\n+ATCCAAATCATCAAACATTA\n'

diff -r 000000000000 -r 078414a1226b test-data/S10.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/S10.fasta Fri Oct 14 21:35:24 2022 +0000

diff -r 000000000000 -r 078414a1226b test-data/S2.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/S2.fasta Fri Oct 14 21:35:24 2022 +0000

diff -r 000000000000 -r 078414a1226b test-data/S3.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/S3.fasta Fri Oct 14 21:35:24 2022 +0000

diff -r 000000000000 -r 078414a1226b test-data/S4.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/S4.fasta Fri Oct 14 21:35:24 2022 +0000

diff -r 000000000000 -r 078414a1226b test-data/S5.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/S5.fasta Fri Oct 14 21:35:24 2022 +0000

diff -r 000000000000 -r 078414a1226b test-data/S6.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/S6.fasta Fri Oct 14 21:35:24 2022 +0000

diff -r 000000000000 -r 078414a1226b test-data/S7.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/S7.fasta Fri Oct 14 21:35:24 2022 +0000

diff -r 000000000000 -r 078414a1226b test-data/S8.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/S8.fasta Fri Oct 14 21:35:24 2022 +0000

diff -r 000000000000 -r 078414a1226b test-data/S9.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/S9.fasta Fri Oct 14 21:35:24 2022 +0000

diff -r 000000000000 -r 078414a1226b test-data/cannot.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cannot.txt Fri Oct 14 21:35:24 2022 +0000

@@ -0,0 +1,15 @@
+g1k_0,g2k_0
+g1k_1,g2k_2
+g1k_1,g2k_3
+g1k_2,g3k_4
+g3k_5,g2k_6
+g4k_5,g2k_9
+g4k_3,g2k_1
+g4k_2,g2k_6
+g3k_1,g2k_1
+g3k_2,g2k_9
+g3k_4,g1k_2
+g3k_9,g1k_9
+g4k_1,g2k_7
+g4k_2,g3k_7
+g2k_7,g3k_1

diff -r 000000000000 -r 078414a1226b test-data/data.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/data.csv Fri Oct 14 21:35:24 2022 +0000

b'@@ -0,0 +1,41 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diff -r 000000000000 -r 078414a1226b test-data/data_split.csv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/data_split.csv Fri Oct 14 21:35:24 2022 +0000

b'@@ -0,0 +1,81 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diff -r 000000000000 -r 078414a1226b test-data/input_coassembly_sorted2.bam

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diff -r 000000000000 -r 078414a1226b test-data/input_coassembly_sorted3.bam

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diff -r 000000000000 -r 078414a1226b test-data/input_coassembly_sorted4.bam

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diff -r 000000000000 -r 078414a1226b test-data/input_coassembly_sorted5.bam

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diff -r 000000000000 -r 078414a1226b test-data/input_multi.fasta.gz

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diff -r 000000000000 -r 078414a1226b test-data/input_multi_sorted1.bam

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diff -r 000000000000 -r 078414a1226b test-data/input_multi_sorted10.bam

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diff -r 000000000000 -r 078414a1226b test-data/input_multi_sorted2.bam

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diff -r 000000000000 -r 078414a1226b test-data/input_multi_sorted3.bam

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diff -r 000000000000 -r 078414a1226b test-data/input_multi_sorted4.bam

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diff -r 000000000000 -r 078414a1226b test-data/input_multi_sorted5.bam

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diff -r 000000000000 -r 078414a1226b test-data/input_multi_sorted6.bam

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diff -r 000000000000 -r 078414a1226b test-data/input_multi_sorted7.bam

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diff -r 000000000000 -r 078414a1226b test-data/input_multi_sorted8.bam

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diff -r 000000000000 -r 078414a1226b test-data/input_multi_sorted9.bam

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diff -r 000000000000 -r 078414a1226b test-data/input_single.bam

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diff -r 000000000000 -r 078414a1226b test-data/input_single.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_single.fasta Fri Oct 14 21:35:24 2022 +0000

diff -r 000000000000 -r 078414a1226b test-data/input_single_2.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_single_2.fasta Fri Oct 14 21:35:24 2022 +0000

diff -r 000000000000 -r 078414a1226b test-data/input_single_3.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_single_3.fasta Fri Oct 14 21:35:24 2022 +0000

diff -r 000000000000 -r 078414a1226b test-data/model.h5

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diff -r 000000000000 -r 078414a1226b test-data/taxonomy.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/taxonomy.tsv Fri Oct 14 21:35:24 2022 +0000

@@ -0,0 +1,40 @@
+g1k_0 13548 genus Treponema A 4 4 4 1.000 d_Bacteria;p_Spirochaetota;c_Spirochaetia;o_Treponematales;f_Treponemataceae;g_Treponema A
+g1k_1 566 species Prevotella intermedia 11 9 6 0.520 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Prevotella;s_Prevotella intermedia
+g1k_2 566 species Prevotella intermedia 15 15 10 0.980 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Prevotella;s_Prevotella intermedia
+g1k_3 206 order Bacteroidales 5 5 5 1.000 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales
+g1k_4 566 species Prevotella intermedia 21 19 11 0.640 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Prevotella;s_Prevotella intermedia
+g1k_5 206 order Bacteroidales 18 16 12 0.730 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales
+g1k_6 206 order Bacteroidales 22 22 14 0.670 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales
+g1k_7 566 species Prevotella intermedia 8 8 5 0.540 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Prevotella;s_Prevotella intermedia
+g1k_8 209 species Bacteroides fragilis 6 5 2 0.640 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Bacteroides;s_Bacteroides fragilis
+g1k_9 565 genus Prevotella 27 25 21 0.870 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Prevotella
+g2k_0 13548 genus Treponema A 3 3 3 1.000 d_Bacteria;p_Spirochaetota;c_Spirochaetia;o_Treponematales;f_Treponemataceae;g_Treponema A
+g2k_1 209 species Bacteroides fragilis 9 9 4 0.930 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Bacteroides;s_Bacteroides fragilis
+g2k_2 565 genus Prevotella 9 9 9 1.000 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Prevotella
+g2k_3 565 genus Prevotella 8 8 7 0.840 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Prevotella
+g2k_4 209 species Bacteroides fragilis 10 8 4 0.500 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Bacteroides;s_Bacteroides fragilis
+g2k_5 8420 species Treponema D porcinum 2 1 1 1.000 d_Bacteria;p_Spirochaetota;c_Spirochaetia;o_Treponematales;f_Treponemataceae;g_Treponema D;s_Treponema D porcinum
+g2k_6 209 species Bacteroides fragilis 58 52 32 0.730 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Bacteroides;s_Bacteroides fragilis
+g2k_7 1193 species Bacteroides eggerthii 14 14 10 0.790 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Bacteroides;s_Bacteroides eggerthii
+g2k_8 566 species Prevotella intermedia 33 32 19 0.600 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Prevotella;s_Prevotella intermedia
+g2k_9 566 species Prevotella intermedia 15 15 7 0.600 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Prevotella;s_Prevotella intermedia
+g3k_0 22555 species UBA1066 sp002316215 3 2 1 0.940 d_Bacteria;p_Firmicutes A;c_Clostridia;o_Lachnospirales;f_Lachnospiraceae;g_UBA1066;s_UBA1066 sp002316215
+g3k_1 11375 species Treponema B denticola A 7 7 5 0.610 d_Bacteria;p_Spirochaetota;c_Spirochaetia;o_Treponematales;f_Treponemataceae;g_Treponema B;s_Treponema B denticola A
+g3k_2 208 genus Bacteroides 22 19 13 0.790 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Bacteroides
+g3k_3 288 family Treponemataceae 5 5 5 1.000 d_Bacteria;p_Spirochaetota;c_Spirochaetia;o_Treponematales;f_Treponemataceae
+g3k_4 208 genus Bacteroides 11 11 7 0.740 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Bacteroides
+g3k_5 208 genus Bacteroides 46 40 24 0.670 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Bacteroides
+g3k_6 2 superkingdom Bacteria 7 7 6 1.000 d_Bacteria
+g3k_7 209 species Bacteroides fragilis 2 2 1 0.500 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Bacteroides;s_Bacteroides fragilis
+g3k_8 566 species Prevotella intermedia 14 14 10 0.750 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Prevotella;s_Prevotella intermedia
+g3k_9 565 genus Prevotella 52 51 45 0.860 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Prevotella
+g4k_0 565 genus Prevotella 10 9 5 0.820 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Prevotella
+g4k_1 565 genus Prevotella 36 35 32 0.890 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Prevotella
+g4k_2 565 genus Prevotella 34 33 31 0.920 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Prevotella
+g4k_3 209 species Bacteroides fragilis 13 12 4 0.560 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Bacteroides;s_Bacteroides fragilis
+g4k_4 209 species Bacteroides fragilis 4 4 3 0.990 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Bacteroides;s_Bacteroides fragilis
+g4k_5 208 genus Bacteroides 24 20 18 0.940 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Bacteroides
+g4k_6 1193 species Bacteroides eggerthii 3 3 3 1.000 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Bacteroides;s_Bacteroides eggerthii
+g4k_7 288 family Treponemataceae 4 4 3 0.670 d_Bacteria;p_Spirochaetota;c_Spirochaetia;o_Treponematales;f_Treponemataceae
+g4k_8 565 genus Prevotella 9 9 7 0.530 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Prevotella
+g4k_9 566 species Prevotella intermedia 11 10 6 0.790 d_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Bacteroidaceae;g_Prevotella;s_Prevotella intermedia

diff -r 000000000000 -r 078414a1226b test-data/taxonomy_10.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/taxonomy_10.tsv Fri Oct 14 21:35:24 2022 +0000

diff -r 000000000000 -r 078414a1226b test-data/taxonomy_2.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/taxonomy_2.tsv Fri Oct 14 21:35:24 2022 +0000

diff -r 000000000000 -r 078414a1226b test-data/taxonomy_3.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/taxonomy_3.tsv Fri Oct 14 21:35:24 2022 +0000

diff -r 000000000000 -r 078414a1226b test-data/taxonomy_4.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/taxonomy_4.tsv Fri Oct 14 21:35:24 2022 +0000

diff -r 000000000000 -r 078414a1226b test-data/taxonomy_5.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/taxonomy_5.tsv Fri Oct 14 21:35:24 2022 +0000

diff -r 000000000000 -r 078414a1226b test-data/taxonomy_6.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/taxonomy_6.tsv Fri Oct 14 21:35:24 2022 +0000

diff -r 000000000000 -r 078414a1226b test-data/taxonomy_7.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/taxonomy_7.tsv Fri Oct 14 21:35:24 2022 +0000

diff -r 000000000000 -r 078414a1226b test-data/taxonomy_8.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/taxonomy_8.tsv Fri Oct 14 21:35:24 2022 +0000

diff -r 000000000000 -r 078414a1226b test-data/taxonomy_9.tsv
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/taxonomy_9.tsv Fri Oct 14 21:35:24 2022 +0000

diff -r 000000000000 -r 078414a1226b test-data/test-db/GTDB

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diff -r 000000000000 -r 078414a1226b test-data/test-db/GTDB.dbtype

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diff -r 000000000000 -r 078414a1226b test-data/test-db/GTDB.index
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db/GTDB.index Fri Oct 14 21:35:24 2022 +0000

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diff -r 000000000000 -r 078414a1226b test-data/test-db/GTDB_mapping
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db/GTDB_mapping Fri Oct 14 21:35:24 2022 +0000

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diff -r 000000000000 -r 078414a1226b test-data/test-db/GTDB_names.dmp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db/GTDB_names.dmp Fri Oct 14 21:35:24 2022 +0000

b'@@ -0,0 +1,45503 @@\n+1\t|\troot\t|\t-\t|\tscientific name\t|\n+2\t|\tBacteria\t|\t-\t|\tscientific name\t|\n+3\t|\tProteobacteria\t|\t-\t|\tscientific name\t|\n+4\t|\tGammaproteobacteria\t|\t-\t|\tscientific name\t|\n+5\t|\tEnterobacterales\t|\t-\t|\tscientific name\t|\n+6\t|\tEnterobacteriaceae\t|\t-\t|\tscientific name\t|\n+7\t|\tEscherichia\t|\t-\t|\tscientific name\t|\n+8\t|\tEscherichia flexneri\t|\t-\t|\tscientific name\t|\n+9\t|\tSalmonella\t|\t-\t|\tscientific name\t|\n+10\t|\tSalmonella enterica\t|\t-\t|\tscientific name\t|\n+11\t|\tFirmicutes\t|\t-\t|\tscientific name\t|\n+12\t|\tBacilli\t|\t-\t|\tscientific name\t|\n+13\t|\tStaphylococcales\t|\t-\t|\tscientific name\t|\n+14\t|\tStaphylococcaceae\t|\t-\t|\tscientific name\t|\n+15\t|\tStaphylococcus\t|\t-\t|\tscientific name\t|\n+16\t|\tStaphylococcus aureus\t|\t-\t|\tscientific name\t|\n+17\t|\tLactobacillales\t|\t-\t|\tscientific name\t|\n+18\t|\tStreptococcaceae\t|\t-\t|\tscientific name\t|\n+19\t|\tStreptococcus\t|\t-\t|\tscientific name\t|\n+20\t|\tStreptococcus pneumoniae\t|\t-\t|\tscientific name\t|\n+21\t|\tKlebsiella\t|\t-\t|\tscientific name\t|\n+22\t|\tKlebsiella pneumoniae\t|\t-\t|\tscientific name\t|\n+23\t|\tActinobacteriota\t|\t-\t|\tscientific name\t|\n+24\t|\tActinomycetia\t|\t-\t|\tscientific name\t|\n+25\t|\tMycobacteriales\t|\t-\t|\tscientific name\t|\n+26\t|\tMycobacteriaceae\t|\t-\t|\tscientific name\t|\n+27\t|\tMycobacterium\t|\t-\t|\tscientific name\t|\n+28\t|\tMycobacterium tuberculosis\t|\t-\t|\tscientific name\t|\n+29\t|\tPseudomonadales\t|\t-\t|\tscientific name\t|\n+30\t|\tPseudomonadaceae\t|\t-\t|\tscientific name\t|\n+31\t|\tPseudomonas\t|\t-\t|\tscientific name\t|\n+32\t|\tPseudomonas aeruginosa\t|\t-\t|\tscientific name\t|\n+33\t|\tMoraxellaceae\t|\t-\t|\tscientific name\t|\n+34\t|\tAcinetobacter\t|\t-\t|\tscientific name\t|\n+35\t|\tAcinetobacter baumannii\t|\t-\t|\tscientific name\t|\n+36\t|\tEscherichia coli\t|\t-\t|\tscientific name\t|\n+37\t|\tFirmicutes A\t|\t-\t|\tscientific name\t|\n+38\t|\tClostridia\t|\t-\t|\tscientific name\t|\n+39\t|\tPeptostreptococcales\t|\t-\t|\tscientific name\t|\n+40\t|\tPeptostreptococcaceae\t|\t-\t|\tscientific name\t|\n+41\t|\tClostridioides\t|\t-\t|\tscientific name\t|\n+42\t|\tClostridioides difficile\t|\t-\t|\tscientific name\t|\n+43\t|\tBurkholderiales\t|\t-\t|\tscientific name\t|\n+44\t|\tNeisseriaceae\t|\t-\t|\tscientific name\t|\n+45\t|\tNeisseria\t|\t-\t|\tscientific name\t|\n+46\t|\tNeisseria meningitidis\t|\t-\t|\tscientific name\t|\n+47\t|\tStreptococcus pyogenes\t|\t-\t|\tscientific name\t|\n+48\t|\tEscherichia dysenteriae\t|\t-\t|\tscientific name\t|\n+49\t|\tEscherichia coli D\t|\t-\t|\tscientific name\t|\n+50\t|\tMycobacterium abscessus\t|\t-\t|\tscientific name\t|\n+51\t|\tBurkholderiaceae\t|\t-\t|\tscientific name\t|\n+52\t|\tBurkholderia\t|\t-\t|\tscientific name\t|\n+53\t|\tBurkholderia mallei\t|\t-\t|\tscientific name\t|\n+54\t|\tListeriaceae\t|\t-\t|\tscientific name\t|\n+55\t|\tListeria\t|\t-\t|\tscientific name\t|\n+56\t|\tListeria monocytogenes\t|\t-\t|\tscientific name\t|\n+57\t|\tCampylobacterota\t|\t-\t|\tscientific name\t|\n+58\t|\tCampylobacteria\t|\t-\t|\tscientific name\t|\n+59\t|\tCampylobacterales\t|\t-\t|\tscientific name\t|\n+60\t|\tCampylobacteraceae\t|\t-\t|\tscientific name\t|\n+61\t|\tCampylobacter D\t|\t-\t|\tscientific name\t|\n+62\t|\tCampylobacter D jejuni\t|\t-\t|\tscientific name\t|\n+63\t|\tEnterococcaceae\t|\t-\t|\tscientific name\t|\n+64\t|\tEnterococcus B\t|\t-\t|\tscientific name\t|\n+65\t|\tEnterococcus B faecium\t|\t-\t|\tscientific name\t|\n+66\t|\tEnterococcus\t|\t-\t|\tscientific name\t|\n+67\t|\tEnterococcus faecalis\t|\t-\t|\tscientific name\t|\n+68\t|\tPseudomonas E\t|\t-\t|\tscientific name\t|\n+69\t|\tPseudomonas E viridiflava\t|\t-\t|\tscientific name\t|\n+70\t|\tVibrionaceae\t|\t-\t|\tscientific name\t|\n+71\t|\tVibrio\t|\t-\t|\tscientific name\t|\n+72\t|\tVibrio parahaemolyticus\t|\t-\t|\tscientific name\t|\n+73\t|\tListeria monocytogenes B\t|\t-\t|\tscientific name\t|\n+74\t|\tStreptococcus agalactiae\t|\t-\t|\tscientific name\t|\n+75\t|\tEnterobacter\t|\t-\t|\tscientific name\t|\n+76\t|\tEnterobacter himalayensis\t|\t-\t|\tscientific name\t|\n+77\t|\tStreptococcus suis\t|\t-\t|\tscientific name\t|\n+78\t|\tVibrio cholerae\t|\t-\t|\tscientific name\t|\n+79\t|\tBordetella\t|\t-\t|\tscientific name\t|\n+80\t|\tBordetella pertussis\t|\t-\t|\tscientific name\t|\n+81\t|\tHelicobacteraceae\t|\t-\t|\tscientific name\t|\n+82\t|\tHelicobacter\t|\t-\t|\tscientific name\t|\n+83\t|\tHelicobacter pylori\t|\t-\t|\tscientific name\t|\n+84\t|\tCampylobacter D coli\t|\t-\t|\tscientific name\t|\n+85\t|\tLegionella'..b'fic name\t|\n+45429\t|\tMethanoregula sp002497485\t|\t-\t|\tscientific name\t|\n+45430\t|\tHaloterrigena salina\t|\t-\t|\tscientific name\t|\n+45431\t|\tFerroglobus\t|\t-\t|\tscientific name\t|\n+45432\t|\tFerroglobus placidus\t|\t-\t|\tscientific name\t|\n+45433\t|\tThermococcus A sp001484685\t|\t-\t|\tscientific name\t|\n+45434\t|\tNatronococcus occultus\t|\t-\t|\tscientific name\t|\n+45435\t|\tCBA1134 sp003021175\t|\t-\t|\tscientific name\t|\n+45436\t|\tHalorientalis persicus\t|\t-\t|\tscientific name\t|\n+45437\t|\tNanoarchaeaceae\t|\t-\t|\tscientific name\t|\n+45438\t|\tNanoarchaeum\t|\t-\t|\tscientific name\t|\n+45439\t|\tNanoarchaeum equitans\t|\t-\t|\tscientific name\t|\n+45440\t|\tB23\t|\t-\t|\tscientific name\t|\n+45441\t|\tB23 sp001593875\t|\t-\t|\tscientific name\t|\n+45442\t|\tB63 sp003601695\t|\t-\t|\tscientific name\t|\n+45443\t|\tPyrobaculum arsenaticum\t|\t-\t|\tscientific name\t|\n+45444\t|\tARS1285 sp002688335\t|\t-\t|\tscientific name\t|\n+45445\t|\tBMS3B sp002897955\t|\t-\t|\tscientific name\t|\n+45446\t|\tMethanomassiliicoccus sp002067635\t|\t-\t|\tscientific name\t|\n+45447\t|\tMethanofastidiosum sp9950u\t|\t-\t|\tscientific name\t|\n+45448\t|\tHalorubrum sp000296615\t|\t-\t|\tscientific name\t|\n+45449\t|\tRBG-16-57-9 sp001775965\t|\t-\t|\tscientific name\t|\n+45450\t|\tHalolamina rubra\t|\t-\t|\tscientific name\t|\n+45451\t|\tHalolamina pelagica B\t|\t-\t|\tscientific name\t|\n+45452\t|\tUBA153 sp003694385\t|\t-\t|\tscientific name\t|\n+45453\t|\t40CM-2-53-6 sp005888635\t|\t-\t|\tscientific name\t|\n+45454\t|\tMP8T-1 sp004524595\t|\t-\t|\tscientific name\t|\n+45455\t|\tSKXI01 sp007128515\t|\t-\t|\tscientific name\t|\n+45456\t|\tMGIIb-O5 sp002726275\t|\t-\t|\tscientific name\t|\n+45457\t|\tNitrosopumilus salaria\t|\t-\t|\tscientific name\t|\n+45458\t|\tMGIIa-K1 sp002701145\t|\t-\t|\tscientific name\t|\n+45459\t|\tMethanofastidiosum sp001587675\t|\t-\t|\tscientific name\t|\n+45460\t|\t40CM-2-53-6 sp005881695\t|\t-\t|\tscientific name\t|\n+45461\t|\tNitrosarchaeum sp003569705\t|\t-\t|\tscientific name\t|\n+45462\t|\tThermococcus gorgonarius\t|\t-\t|\tscientific name\t|\n+45463\t|\tMethanoculleus sp000691865\t|\t-\t|\tscientific name\t|\n+45464\t|\tHalobellus sp003665925\t|\t-\t|\tscientific name\t|\n+45465\t|\tSMTZ1-45 sp004376265\t|\t-\t|\tscientific name\t|\n+45466\t|\tNitrosopumilus sediminis\t|\t-\t|\tscientific name\t|\n+45467\t|\tStaphylothermus hellenicus\t|\t-\t|\tscientific name\t|\n+45468\t|\tMethanomethylovorans sp001896725\t|\t-\t|\tscientific name\t|\n+45469\t|\tMGIIb-O3 sp002731195\t|\t-\t|\tscientific name\t|\n+45470\t|\tMethanocaldococcus A infernus\t|\t-\t|\tscientific name\t|\n+45471\t|\tMethanobrevibacter A sp900320955\t|\t-\t|\tscientific name\t|\n+45472\t|\tXQ-INN-246\t|\t-\t|\tscientific name\t|\n+45473\t|\tXQ-INN-246 sp006543045\t|\t-\t|\tscientific name\t|\n+45474\t|\tMGIIa-L3 sp002694585\t|\t-\t|\tscientific name\t|\n+45475\t|\tNitrosopumilus sp006740685\t|\t-\t|\tscientific name\t|\n+45476\t|\tHalorussus rarus\t|\t-\t|\tscientific name\t|\n+45477\t|\tB75-G9\t|\t-\t|\tscientific name\t|\n+45478\t|\tB75-G9 sp003661465\t|\t-\t|\tscientific name\t|\n+45479\t|\tJdFR-22\t|\t-\t|\tscientific name\t|\n+45480\t|\tJdFR-22 sp002010045\t|\t-\t|\tscientific name\t|\n+45481\t|\tHalogranum sp004116405\t|\t-\t|\tscientific name\t|\n+45482\t|\tHalorussus amylolyticus\t|\t-\t|\tscientific name\t|\n+45483\t|\tNitrosopumilus sp002788515\t|\t-\t|\tscientific name\t|\n+45484\t|\tEX4572-165\t|\t-\t|\tscientific name\t|\n+45485\t|\tEX4572-165 sp002254885\t|\t-\t|\tscientific name\t|\n+45486\t|\tB47-G15\t|\t-\t|\tscientific name\t|\n+45487\t|\tB47-G15\t|\t-\t|\tscientific name\t|\n+45488\t|\tB47-G15 sp003660975\t|\t-\t|\tscientific name\t|\n+45489\t|\tThalassarchaeum sp002727275\t|\t-\t|\tscientific name\t|\n+45490\t|\tQENH01\t|\t-\t|\tscientific name\t|\n+45491\t|\tQENH01 sp003336485\t|\t-\t|\tscientific name\t|\n+45492\t|\tHEL-GB-A\t|\t-\t|\tscientific name\t|\n+45493\t|\tHEL-GB-A\t|\t-\t|\tscientific name\t|\n+45494\t|\tHEL-GB-A sp005191415\t|\t-\t|\tscientific name\t|\n+45495\t|\tHalonotius sp006861665\t|\t-\t|\tscientific name\t|\n+45496\t|\tNatrinema salaciae\t|\t-\t|\tscientific name\t|\n+45497\t|\tSBBD01\t|\t-\t|\tscientific name\t|\n+45498\t|\tSBBD01\t|\t-\t|\tscientific name\t|\n+45499\t|\tSBBD01 sp005239845\t|\t-\t|\tscientific name\t|\n+45500\t|\tGW2011-AR5 sp10154u\t|\t-\t|\tscientific name\t|\n+45501\t|\tMethanotorris formicicus\t|\t-\t|\tscientific name\t|\n+45502\t|\tHaladaptatus cibarius\t|\t-\t|\tscientific name\t|\n+45503\t|\tDTU008 sp002498285\t|\t-\t|\tscientific name\t|\n'

diff -r 000000000000 -r 078414a1226b test-data/test-db/GTDB_nodes.dmp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test-db/GTDB_nodes.dmp Fri Oct 14 21:35:24 2022 +0000

b'@@ -0,0 +1,45503 @@\n+1\t|\t1\t|\tno rank\t|\t-\t|\n+2\t|\t1\t|\tsuperkingdom\t|\t-\t|\n+3\t|\t2\t|\tphylum\t|\t-\t|\n+4\t|\t3\t|\tclass\t|\t-\t|\n+5\t|\t4\t|\torder\t|\t-\t|\n+6\t|\t5\t|\tfamily\t|\t-\t|\n+7\t|\t6\t|\tgenus\t|\t-\t|\n+8\t|\t7\t|\tspecies\t|\t-\t|\n+9\t|\t6\t|\tgenus\t|\t-\t|\n+10\t|\t9\t|\tspecies\t|\t-\t|\n+11\t|\t2\t|\tphylum\t|\t-\t|\n+12\t|\t11\t|\tclass\t|\t-\t|\n+13\t|\t12\t|\torder\t|\t-\t|\n+14\t|\t13\t|\tfamily\t|\t-\t|\n+15\t|\t14\t|\tgenus\t|\t-\t|\n+16\t|\t15\t|\tspecies\t|\t-\t|\n+17\t|\t12\t|\torder\t|\t-\t|\n+18\t|\t17\t|\tfamily\t|\t-\t|\n+19\t|\t18\t|\tgenus\t|\t-\t|\n+20\t|\t19\t|\tspecies\t|\t-\t|\n+21\t|\t6\t|\tgenus\t|\t-\t|\n+22\t|\t21\t|\tspecies\t|\t-\t|\n+23\t|\t2\t|\tphylum\t|\t-\t|\n+24\t|\t23\t|\tclass\t|\t-\t|\n+25\t|\t24\t|\torder\t|\t-\t|\n+26\t|\t25\t|\tfamily\t|\t-\t|\n+27\t|\t26\t|\tgenus\t|\t-\t|\n+28\t|\t27\t|\tspecies\t|\t-\t|\n+29\t|\t4\t|\torder\t|\t-\t|\n+30\t|\t29\t|\tfamily\t|\t-\t|\n+31\t|\t30\t|\tgenus\t|\t-\t|\n+32\t|\t31\t|\tspecies\t|\t-\t|\n+33\t|\t29\t|\tfamily\t|\t-\t|\n+34\t|\t33\t|\tgenus\t|\t-\t|\n+35\t|\t34\t|\tspecies\t|\t-\t|\n+36\t|\t7\t|\tspecies\t|\t-\t|\n+37\t|\t2\t|\tphylum\t|\t-\t|\n+38\t|\t37\t|\tclass\t|\t-\t|\n+39\t|\t38\t|\torder\t|\t-\t|\n+40\t|\t39\t|\tfamily\t|\t-\t|\n+41\t|\t40\t|\tgenus\t|\t-\t|\n+42\t|\t41\t|\tspecies\t|\t-\t|\n+43\t|\t4\t|\torder\t|\t-\t|\n+44\t|\t43\t|\tfamily\t|\t-\t|\n+45\t|\t44\t|\tgenus\t|\t-\t|\n+46\t|\t45\t|\tspecies\t|\t-\t|\n+47\t|\t19\t|\tspecies\t|\t-\t|\n+48\t|\t7\t|\tspecies\t|\t-\t|\n+49\t|\t7\t|\tspecies\t|\t-\t|\n+50\t|\t27\t|\tspecies\t|\t-\t|\n+51\t|\t43\t|\tfamily\t|\t-\t|\n+52\t|\t51\t|\tgenus\t|\t-\t|\n+53\t|\t52\t|\tspecies\t|\t-\t|\n+54\t|\t17\t|\tfamily\t|\t-\t|\n+55\t|\t54\t|\tgenus\t|\t-\t|\n+56\t|\t55\t|\tspecies\t|\t-\t|\n+57\t|\t2\t|\tphylum\t|\t-\t|\n+58\t|\t57\t|\tclass\t|\t-\t|\n+59\t|\t58\t|\torder\t|\t-\t|\n+60\t|\t59\t|\tfamily\t|\t-\t|\n+61\t|\t60\t|\tgenus\t|\t-\t|\n+62\t|\t61\t|\tspecies\t|\t-\t|\n+63\t|\t17\t|\tfamily\t|\t-\t|\n+64\t|\t63\t|\tgenus\t|\t-\t|\n+65\t|\t64\t|\tspecies\t|\t-\t|\n+66\t|\t63\t|\tgenus\t|\t-\t|\n+67\t|\t66\t|\tspecies\t|\t-\t|\n+68\t|\t30\t|\tgenus\t|\t-\t|\n+69\t|\t68\t|\tspecies\t|\t-\t|\n+70\t|\t5\t|\tfamily\t|\t-\t|\n+71\t|\t70\t|\tgenus\t|\t-\t|\n+72\t|\t71\t|\tspecies\t|\t-\t|\n+73\t|\t55\t|\tspecies\t|\t-\t|\n+74\t|\t19\t|\tspecies\t|\t-\t|\n+75\t|\t6\t|\tgenus\t|\t-\t|\n+76\t|\t75\t|\tspecies\t|\t-\t|\n+77\t|\t19\t|\tspecies\t|\t-\t|\n+78\t|\t71\t|\tspecies\t|\t-\t|\n+79\t|\t51\t|\tgenus\t|\t-\t|\n+80\t|\t79\t|\tspecies\t|\t-\t|\n+81\t|\t59\t|\tfamily\t|\t-\t|\n+82\t|\t81\t|\tgenus\t|\t-\t|\n+83\t|\t82\t|\tspecies\t|\t-\t|\n+84\t|\t61\t|\tspecies\t|\t-\t|\n+85\t|\t4\t|\torder\t|\t-\t|\n+86\t|\t85\t|\tfamily\t|\t-\t|\n+87\t|\t86\t|\tgenus\t|\t-\t|\n+88\t|\t87\t|\tspecies\t|\t-\t|\n+89\t|\t3\t|\tclass\t|\t-\t|\n+90\t|\t89\t|\torder\t|\t-\t|\n+91\t|\t90\t|\tfamily\t|\t-\t|\n+92\t|\t91\t|\tgenus\t|\t-\t|\n+93\t|\t92\t|\tspecies\t|\t-\t|\n+94\t|\t45\t|\tspecies\t|\t-\t|\n+95\t|\t5\t|\tfamily\t|\t-\t|\n+96\t|\t95\t|\tgenus\t|\t-\t|\n+97\t|\t96\t|\tspecies\t|\t-\t|\n+98\t|\t15\t|\tspecies\t|\t-\t|\n+99\t|\t12\t|\torder\t|\t-\t|\n+100\t|\t99\t|\tfamily\t|\t-\t|\n+101\t|\t100\t|\tgenus\t|\t-\t|\n+102\t|\t101\t|\tspecies\t|\t-\t|\n+103\t|\t17\t|\tfamily\t|\t-\t|\n+104\t|\t103\t|\tgenus\t|\t-\t|\n+105\t|\t104\t|\tspecies\t|\t-\t|\n+106\t|\t21\t|\tspecies\t|\t-\t|\n+107\t|\t6\t|\tgenus\t|\t-\t|\n+108\t|\t107\t|\tspecies\t|\t-\t|\n+109\t|\t6\t|\tgenus\t|\t-\t|\n+110\t|\t109\t|\tspecies\t|\t-\t|\n+111\t|\t6\t|\tgenus\t|\t-\t|\n+112\t|\t111\t|\tspecies\t|\t-\t|\n+113\t|\t21\t|\tspecies\t|\t-\t|\n+114\t|\t4\t|\torder\t|\t-\t|\n+115\t|\t114\t|\tfamily\t|\t-\t|\n+116\t|\t115\t|\tgenus\t|\t-\t|\n+117\t|\t116\t|\tspecies\t|\t-\t|\n+118\t|\t82\t|\tspecies\t|\t-\t|\n+119\t|\t52\t|\tspecies\t|\t-\t|\n+120\t|\t2\t|\tphylum\t|\t-\t|\n+121\t|\t120\t|\tclass\t|\t-\t|\n+122\t|\t121\t|\torder\t|\t-\t|\n+123\t|\t122\t|\tfamily\t|\t-\t|\n+124\t|\t123\t|\tgenus\t|\t-\t|\n+125\t|\t124\t|\tspecies\t|\t-\t|\n+126\t|\t24\t|\torder\t|\t-\t|\n+127\t|\t126\t|\tfamily\t|\t-\t|\n+128\t|\t127\t|\tgenus\t|\t-\t|\n+129\t|\t128\t|\tspecies\t|\t-\t|\n+130\t|\t24\t|\torder\t|\t-\t|\n+131\t|\t130\t|\tfamily\t|\t-\t|\n+132\t|\t131\t|\tgenus\t|\t-\t|\n+133\t|\t132\t|\tspecies\t|\t-\t|\n+134\t|\t101\t|\tspecies\t|\t-\t|\n+135\t|\t19\t|\tspecies\t|\t-\t|\n+136\t|\t15\t|\tspecies\t|\t-\t|\n+137\t|\t99\t|\tfamily\t|\t-\t|\n+138\t|\t137\t|\tgenus\t|\t-\t|\n+139\t|\t138\t|\tspecies\t|\t-\t|\n+140\t|\t138\t|\tspecies\t|\t-\t|\n+141\t|\t34\t|\tspecies\t|\t-\t|\n+142\t|\t68\t|\tspecies\t|\t-\t|\n+143\t|\t82\t|\tspecies\t|\t-\t|\n+144\t|\t4\t|\torder\t|\t-\t|\n+145\t|\t144\t|\tfamily\t|\t-\t|\n+146\t|\t145\t|\tgenus\t|\t-\t|\n+147\t|\t146\t|\tspecies\t|\t-\t|\n+148\t|\t52\t|\tspecies\t|\t-\t|\n+149\t|\t101\t|\tspecies\t|\t-\t|\n+150\t|\t26\t|\tgenus\t|\t-\t|\n+151\t|\t150\t|\tspecies\t|\t-\t|\n+152\t|\t103\t|\tgenus\t|\t-\t|\n+153\t|\t152\t|\tspecies\t|\t-\t|\n+154\t|\t15\t|\tspecies\t|\t-\t|\n+155\t|\t101\t|\tspecies\t|\t-\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t-\t|\n+45496\t|\t43092\t|\tspecies\t|\t-\t|\n+45497\t|\t42886\t|\tfamily\t|\t-\t|\n+45498\t|\t45497\t|\tgenus\t|\t-\t|\n+45499\t|\t45498\t|\tspecies\t|\t-\t|\n+45500\t|\t44552\t|\tspecies\t|\t-\t|\n+45501\t|\t44073\t|\tspecies\t|\t-\t|\n+45502\t|\t43006\t|\tspecies\t|\t-\t|\n+45503\t|\t42810\t|\tspecies\t|\t-\t|\n'

diff -r 000000000000 -r 078414a1226b test-data/test_database.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_database.loc Fri Oct 14 21:35:24 2022 +0000

@@ -0,0 +1,6 @@
+# Tab separated with 4 columns:
+# - value (Galaxy records this in the Galaxy DB)
+# - name (Galaxy shows this in the UI)
+# - value (Galaxy records this in the Galaxy DB)
+# - path (folder name containing the Kraken DB)
+test-db "Test Database" test-db ${__HERE__}/test-db
\ No newline at end of file

diff -r 000000000000 -r 078414a1226b tool-data/gtdb.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/gtdb.loc.sample Fri Oct 14 21:35:24 2022 +0000

@@ -0,0 +1,7 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of metagenomics files.
+#file has this format (white space characters are TAB characters)
+# - db-build-version-date
+# - db-name
+# - build
+# - /path/to/data
\ No newline at end of file

diff -r 000000000000 -r 078414a1226b tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri Oct 14 21:35:24 2022 +0000

@@ -0,0 +1,6 @@
+<tables>
+    <table name="gtdb" comment_char="#">
+        <columns>value, name, dbkey, path</columns>
+        <file path="tool-data/gtdb.loc" />
+    </table>
+</tables>

diff -r 000000000000 -r 078414a1226b tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Fri Oct 14 21:35:24 2022 +0000

@@ -0,0 +1,6 @@
+<tables>
+    <table name="gtdb" comment_char="#">
+        <columns>value, name, dbkey, path</columns>
+        <file path="${__HERE__}/test-data/test_database.loc" />
+    </table>
+</tables>
\ No newline at end of file