# HG changeset patch
# User iuc
# Date 1705097499 0
# Node ID 3cdb96f2855dd88578ac77efd66ec44aa6893ab4

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx commit 4a6561ed00e004260be3f3c29d81e814c60e20af

diff -r 000000000000 -r 3cdb96f2855d macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Jan 12 22:11:39 2024 +0000
@@ -0,0 +1,22 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">ncbi-fcs-gx</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <token name="@TOOL_VERSION@">0.5.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.05</token>
+    <xml name="edam_ontology">
+        <edam_operations>
+            <edam_operation>operation_3187</edam_operation>
+        </edam_operations>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1101/2023.06.02.543519</citation>
+            <yield/>
+        </citations>
+    </xml>
+</macros>
diff -r 000000000000 -r 3cdb96f2855d ncbi_fcs_gx.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ncbi_fcs_gx.xml	Fri Jan 12 22:11:39 2024 +0000
@@ -0,0 +1,167 @@
+<tool id="ncbi_fcs_gx" name="NCBI FCS GX" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>detects contamination from foreign organisms in genome sequences</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="edam_ontology"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+GX_NUM_CORES=\${GALAXY_SLOTS:-2}
+#if $mode.mode_selector == "screen"
+    ## copy data to local storage
+    #set manifest_pathname = $mode.screen_adv.database.fields.name
+    #if $mode.config_tag.fields.use_source_manifest == "1"
+        #set manifest_pathname = $mode.screen_adv.database.fields.source_manifest
+    #end if
+    mkdir -p '$mode.config_tag.fields.node_cache_dir' &&
+    sync_files.py get --mft '$manifest_pathname' --dir '$mode.config_tag.fields.node_cache_dir' > /dev/null 2>&1 &&
+    ## run gx
+    run_gx.py
+    #if $mode.config_tag.fields.phone_home == "1"
+        --phone-home-label '$mode.config_tag.fields.phone_home_label'
+    #end if
+        --fasta '$mode.fasta'
+    #if $mode.id.id_selector == "gx_div"
+        --tax-id '1'
+        --div '$mode.id.div'
+    #else
+        --tax-id '$mode.id.tax_id'
+    #end if
+    #if $mode.species != ""
+        --species '$mode.species'
+    #end if
+        --split-fasta '$mode.screen_adv.split_fasta'
+    #if $mode.screen_adv.div:
+        --div '$mode.screen_adv.div'
+    #end if
+        --gx-db '$mode.config_tag.fields.node_cache_dir'
+        --out-basename output
+        --action-report true
+        --generate-logfile false
+#elif $mode.mode_selector == "clean"
+    ## run gx
+    gx clean-genome
+        --input '$mode.input'
+        --action-report '$mode.action_report'
+        --contam-fasta-out 'contam.fa'
+        --min-seq-len '$mode.min_seq_len'
+        --output 'clean.fa'
+#end if
+    ]]></command>
+    <environment_variables>
+        <environment_variable name="GX_ALIGN_EXCLUDE_TAXA">$getVar('mode.screen_adv.gx_align_exclude_taxa', '')</environment_variable>
+        <environment_variable name="GX_EXTRA_CONTAM_DIVS"><![CDATA[#echo ','.join($getVar('mode.screen_adv.gx_extra_contam_divs', []))]]></environment_variable>
+    </environment_variables>
+    <inputs>
+        <conditional name="mode">
+            <param name="mode_selector" type="select" label="Choose the mode">
+                <option value="screen" selected="true">Screen genome</option>
+                <option value="clean">Clean genome</option>
+            </param>
+            <when value="screen">
+                <!-- value, name, use_source_manifest, phone_home, phone_home_label, node_cache_dir -->
+                <param name="config_tag" type="select" label="Database">
+                    <options from_data_table="ncbi_fcs_gx_config">
+                        <filter type="sort_by" name="sorted_description" column="1"/>
+                    </options>
+                    <validator message="No database is available" type="no_options"/>
+                </param>
+                <param argument="--fasta" type="data" format="fasta" label="Input file (Fasta file)" help="To detect contamination from foreign organisms, a genome assembly in a fasta file."/>
+                <conditional name="id">
+                    <param name="id_selector" type="select" label="Taxonomy entry">
+                        <option value="gx_div" selected="true">GX Division</option>
+                        <option value="ncbi_tax">NCBI Taxonomic identifier</option>
+                    </param>
+                    <when value="gx_div">
+                        <param argument="--div" type="select">
+                            <options from_data_table="ncbi_fcs_gx_divisions">
+                                <filter type="param_value" ref="config_tag" column="1" />
+                                <filter type="sort_by" name="sorted_description" column="2" />
+                            </options>
+                            <validator message="No GX Divisions are available" type="no_options"/>
+                        </param>
+                    </when>
+                    <when value="ncbi_tax">
+                        <!-- https://www.ncbi.nlm.nih.gov/taxonomy -->
+                        <param argument="--tax-id" type="text" label="Taxonomic identifier" help="The appropriate tax-id for your genome assembly.  The appropriate tax-id for an organism can be retrieved from the NCBI Taxonomy website."/>
+                    </when>
+                </conditional>
+                <param argument="--species" type="text" optional="true" label="Species binomial name"/>
+                <section name="screen_adv" title="Advanced options">
+                    <!-- comma separated list of taxa to ignore in GX_ALIGN_EXCLUDE_TAXA environment variable -->
+                    <param name="gx_align_exclude_taxa" type="text" value="" optional="true" label="Taxonomic identifier(s) to exclude" help="Multiple tax-ids may be provided as a comma-separated list.">
+                        <validator type="regex" message="comma separated integers">^\s*\d+\s*(,\s*\d+\s*)*$</validator>
+                        <sanitizer invalid_char="">
+                            <valid initial="string.digits">
+                                <add value=","/>
+                            </valid>
+                        </sanitizer>
+                    </param>
+                    <param name="gx_extra_contam_divs" type="select" multiple="true" optional="true" label="Additional contaminants to identify" help="Multiple gx-divisions may be selected.">
+                        <options from_data_table="ncbi_fcs_gx_divisions">
+                            <filter type="param_value" ref="config_tag" column="1" />
+                            <filter type="sort_by" name="sorted_description" column="2" />
+                        </options>
+                        <validator message="No GX Divisions are available" type="no_options"/>
+                    </param>
+                    <param argument="--split-fasta" type="boolean" checked="true" optional="true" label="Split fasta sequences on N-runs of length at least 10"/>
+                    <param argument="--div" type="text" value="" optional="true" label="BLAST-div of the tax-id" help="from 'NCBI BLAST name' on taxon Info page"/>
+                    <param name="database" type="select" label="Database location">
+                        <options from_data_table="ncbi_fcs_gx_databases">
+                            <filter type="param_value" ref="config_tag" column="0"/>
+                        </options>
+                        <validator message="No database location is available" type="no_options"/>
+                    </param>
+                </section>
+            </when>
+            <when value="clean">
+                <param argument="--input" type="data" format="fasta" label="Input file (Fasta file)" help="To detect contamination from foreign organisms, a genome assembly in a fasta file."/>
+                <param argument="--action-report" type="data" format="tabular" label="Select Action report"/>
+                <param argument="--min-seq-len" type="integer" value="200" label="Minimumm sequence length to keep"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <!-- mode == screen -->
+        <data name="taxonomy_report" format="tabular" from_work_dir="output.taxonomy.rpt" label="${tool.name} on ${on_string}: Taxonomy report">
+            <filter>mode['mode_selector'] == 'screen'</filter>
+        </data>
+        <data name="action_report" format="tabular" from_work_dir="output.fcs_gx_report.txt" label="${tool.name} on ${on_string}: Action report">
+            <filter>mode['mode_selector'] == 'screen'</filter>
+        </data>
+        <!-- mode == clean -->
+        <data name="contam_fasta" format="fasta" from_work_dir="contam.fa" label="${tool.name} on ${on_string}: Fasta for EXCLUDE entries">
+            <filter>mode['mode_selector'] == 'clean'</filter>
+        </data>
+        <data name="clean_fasta" format="fasta" from_work_dir="clean.fa" metadata_source="mode.input" label="${tool.name} on ${on_string}: Cleaned Fasta">
+            <filter>mode['mode_selector'] == 'clean'</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <param name="mode_selector" value="screen"/>
+            <param name="config_tag" value="test-only" />
+            <param name="id_selector" value="ncbi_tax"/>
+            <param name="fasta" value="fcsgx_test.fa.gz" ftype="fasta"/>
+            <param name="tax_id" value="6973"/>
+            <output name="taxonomy_report" file="output.taxonomy.rpt" compare="diff" lines_diff="2" />
+            <output name="action_report" file="output.fcs_gx_report.txt" compare="diff" lines_diff="2" />
+        </test>
+        <test expect_num_outputs="2">
+            <param name="mode_selector" value="clean"/>
+            <param name="id_selector" value="ncbi_tax"/>
+            <param name="input" value="fcsgx_test.fa.gz" ftype="fasta"/>
+            <param name="action_report" value="output.fcs_gx_report.txt" ftype="tabular"/>
+            <output name="contam_fasta" decompress="true" file="output.contam.fa.gz" ftype="fasta" />
+            <output name="clean_fasta" decompress="true" file="output.clean.fa.gz" ftype="fasta" />
+        </test>
+    </tests>
+    <help><![CDATA[
+    FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). The FCS-GX executable retrieves a Docker or Singularity container and runs a pipeline to align sequences to a large database of NCBI genomes through modified k-mer seeds and assign a most likely taxonomic division.
+
+    FCS-GX classifies sequences as contaminant when their taxonomic assignment is different from the user provided taxonomic identifier. A contamination summary provides an overview of observed contaminant divisions, counts, and total sizes, and an action report provides details and recommended actions for each problematic sequence.
+
+    https://github.com/ncbi/fcs/wiki/FCS-GX
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
diff -r 000000000000 -r 3cdb96f2855d test-data/fcsgx_test.fa.gz
Binary file test-data/fcsgx_test.fa.gz has changed
diff -r 000000000000 -r 3cdb96f2855d test-data/ncbi_fcs_gx_config.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ncbi_fcs_gx_config.tsv	Fri Jan 12 22:11:39 2024 +0000
@@ -0,0 +1,4 @@
+## NCBI FCS GX Tool Config
+# 
+#tag	description	use_source_manifest	phone_home	phone_home_label	node_cache_dir
+test-only	Testing GX database	1	0		/tmp/gxdb
diff -r 000000000000 -r 3cdb96f2855d test-data/ncbi_fcs_gx_databases.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ncbi_fcs_gx_databases.loc	Fri Jan 12 22:11:39 2024 +0000
@@ -0,0 +1,2 @@
+#tag	source_manifest	local_manifest
+test-only	https://ncbi-fcs-gx.s3.amazonaws.com/gxdb/test-only/test-only.manifest	<UNUSED>
diff -r 000000000000 -r 3cdb96f2855d test-data/ncbi_fcs_gx_divisions.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ncbi_fcs_gx_divisions.tsv	Fri Jan 12 22:11:39 2024 +0000
@@ -0,0 +1,3 @@
+#gx_div	tag	description
+prok:CFB group bacteria	test-only	Bacteria - CFB group bacteria
+unkn:unknown	test-only	Unknown / Unclassified
diff -r 000000000000 -r 3cdb96f2855d test-data/output.clean.fa.gz
Binary file test-data/output.clean.fa.gz has changed
diff -r 000000000000 -r 3cdb96f2855d test-data/output.contam.fa.gz
Binary file test-data/output.contam.fa.gz has changed
diff -r 000000000000 -r 3cdb96f2855d test-data/output.fcs_gx_report.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.fcs_gx_report.txt	Fri Jan 12 22:11:39 2024 +0000
@@ -0,0 +1,7 @@
+##[["FCS genome report", 2, 1], {"git-rev": "+branch--", "run-date": "Wed Jan 10 08:58:52 2024", "db": {"build-date": "2022-11-03", "seqs": 3042, "Gbp": 0.28336}, "run-info": {"agg-cvg": 0.358706, "asserted-div": "anml:insects", "inferred-primary-divs": ["prok:CFB group bacteria"], "corrected-primary-divs": ["anml:insects"]}}]
+#seq_id	start_pos	end_pos	seq_len	action	div	agg_cont_cov	top_tax_name
+JPZV02005859.1	1	705930	705930	REVIEW	prok:CFB group bacteria	22	Bacteroides xylanisolvens
+JPZV02009577.1	1	600722	600722	EXCLUDE	prok:CFB group bacteria	52	Bacteroides caecimuris
+JPZV02016362.1	1	432265	432265	EXCLUDE	prok:CFB group bacteria	45	Bacteroides salyersiae
+JPZV02031416.1	1	170387	170387	REVIEW	prok:CFB group bacteria	18	Bacteroides sp. CBA7301
+JPZV02034235.1	1	131158	131158	REVIEW	prok:CFB group bacteria	24	Bacteroides faecichinchillae
diff -r 000000000000 -r 3cdb96f2855d test-data/output.taxonomy.rpt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.taxonomy.rpt	Fri Jan 12 22:11:39 2024 +0000
@@ -0,0 +1,8 @@
+##[["GX taxonomy analysis report", 3, 1], {"git-rev": "+branch--", "run-date": "Wed Jan 10 08:58:52 2024", "db": {"build-date": "2022-11-03", "seqs": 3042, "Gbp": 0.28336}, "run-info": {"agg-cvg": 0.358706, "asserted-div": "anml:insects", "inferred-primary-divs": ["prok:CFB group bacteria"], "corrected-primary-divs": ["anml:insects"]}}]
+#seq-id	seq-len	(xp,lc,co,n,xc)-len	cvg-by-all	sep1	tax-name-1	tax-id-1	div-1	cvg-by-div-1	cvg-by-tax-1	score-1	sep2	tax-id-2	div-2	cvg-by-div-2	cvg-by-tax-2	score-2	sep3	tax-id-3	div-3	cvg-by-div-3	cvg-by-tax-3	score-3	sep4	tax-id-4	div-4	cvg-by-div-4	cvg-by-tax-4	score-4	sep5	reserved	result	div	div_pct_cvg
+JPZV02005859.1	705930	0,1139,0,0,0	159470	|	Bacteroides xylanisolvens	371601	prok:CFB group bacteria	159470	49227	393	|	1796613	prok:CFB group bacteria	159470	48051	387	|						|						|	n/a	low-coverage	prok:CFB group bacteria	23
+JPZV02009577.1	600722	0,65,0,0,0	316464	|	Bacteroides caecimuris	1796613	prok:CFB group bacteria	316464	137645	782	|	371601	prok:CFB group bacteria	316464	120328	757	|						|						|	n/a	contaminant(div)	prok:CFB group bacteria	53
+JPZV02016362.1	432265	0,0,0,0,0	197253	|	Bacteroides salyersiae	291644	prok:CFB group bacteria	197253	74527	520	|	246787	prok:CFB group bacteria	197253	74971	512	|						|						|	n/a	contaminant(div)	prok:CFB group bacteria	46
+JPZV02031416.1	170387	0,60,0,0,0	32395	|	Bacteroides sp. CBA7301	2715212	prok:CFB group bacteria	32395	13706	205	|	1297750	prok:CFB group bacteria	32395	12253	201	|						|						|	n/a	low-coverage	prok:CFB group bacteria	19
+JPZV02034235.1	131158	0,0,0,0,0	33221	|	Bacteroides faecichinchillae	871325	prok:CFB group bacteria	33221	17243	230	|	1121098	prok:CFB group bacteria	33221	15138	222	|						|						|	n/a	low-coverage	prok:CFB group bacteria	25
+JPZV02046037.1	26753	0,0,0,0,0	2720	|	Bacteroides graminisolvens DSM 19988 = JCM 15093	1121097	prok:CFB group bacteria	2720	912	45	|	28111	prok:CFB group bacteria	2720	821	45	|						|						|	n/a	low-coverage	prok:CFB group bacteria	10
diff -r 000000000000 -r 3cdb96f2855d tool-data/ncbi_fcs_gx_config.tsv.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/ncbi_fcs_gx_config.tsv.sample	Fri Jan 12 22:11:39 2024 +0000
@@ -0,0 +1,5 @@
+## NCBI FCS GX Tool Configuration
+# 
+#tag	description	use_source_manifest	phone_home	phone_home_label	node_cache_dir
+#all	Complete GX database	0	0		/tmp/gxdb
+#test-only	Testing GX database	0	1	usegalaxy.org	/tmp/gxdb
diff -r 000000000000 -r 3cdb96f2855d tool-data/ncbi_fcs_gx_databases.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/ncbi_fcs_gx_databases.loc.sample	Fri Jan 12 22:11:39 2024 +0000
@@ -0,0 +1,8 @@
+## NCBI FCS GX Databases
+# 
+#tag	manifest	path
+#r2022-01-24	https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/r2022-01-24/all.manifest	/big/data/dir/ncbi_fcs_gx_databases/r2022-01-24/all.manifest
+#r2022-07-08	https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/r2022-07-08/all.manifest	/big/data/dir/ncbi_fcs_gx_databases/r2022-07-08/all.manifest
+#r2023-01-24	https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/r2023-01-24/all.manifest	/big/data/dir/ncbi_fcs_gx_databases/r2023-01-24/all.manifest
+#latest	https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/latest/all.manifest	/big/data/dir/ncbi_fcs_gx_databases/latest/all.manifest
+#test-only	https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.manifest	/big/data/dir/ncbi_fcs_gx_databases/test-only/test-only.manifest
diff -r 000000000000 -r 3cdb96f2855d tool-data/ncbi_fcs_gx_divisions.tsv.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/ncbi_fcs_gx_divisions.tsv.sample	Fri Jan 12 22:11:39 2024 +0000
@@ -0,0 +1,64 @@
+#gx_div	tag	description
+#anml:amphibians	latest	Animals (Metazoa) - amphibians
+#anml:basal metazoans	latest	Animals (Metazoa) - basal metazoans
+#anml:birds	latest	Animals (Metazoa) - birds
+#anml:brachiopods	latest	Animals (Metazoa) - brachiopods
+#anml:crustaceans	latest	Animals (Metazoa) - crustaceans
+#anml:echinoderms	latest	Animals (Metazoa) - echinoderms
+#anml:fishes	latest	Animals (Metazoa) - fishes
+#anml:insects	latest	Animals (Metazoa) - insects
+#anml:mammals	latest	Animals (Metazoa) - mammals
+#anml:marsupials	latest	Animals (Metazoa) - marsupials
+#anml:molluscs	latest	Animals (Metazoa) - molluscs
+#anml:nematodes	latest	Animals (Metazoa) - nematodes
+#anml:primates	latest	Animals (Metazoa) - primates
+#anml:reptiles	latest	Animals (Metazoa) - reptiles
+#anml:rodents	latest	Animals (Metazoa) - rodents
+#anml:rotifers	latest	Animals (Metazoa) - rotifers
+#anml:tardigrades	latest	Animals (Metazoa) - tardigrades
+#anml:worms	latest	Animals (Metazoa) - worms
+#arch:archaea	latest	Archaea - archaea
+#prok:CFB group bacteria	latest	Bacteria - CFB group bacteria
+#prok:GNS bacteria	latest	Bacteria - GNS bacteria
+#prok:a-proteobacteria	latest	Bacteria - a-proteobacteria
+#prok:actinobacteria	latest	Bacteria - actinobacteria
+#prok:aquificales	latest	Bacteria - aquificales
+#prok:b-proteobacteria	latest	Bacteria - b-proteobacteria
+#prok:bacteria	latest	Bacteria - bacteria
+#prok:chlamydias	latest	Bacteria - chlamydias
+#prok:cyanobacteria	latest	Bacteria - cyanobacteria
+#prok:d-proteobacteria	latest	Bacteria - d-proteobacteria
+#prok:firmicutes	latest	Bacteria - firmicutes
+#prok:fusobacteria	latest	Bacteria - fusobacteria
+#prok:g-proteobacteria	latest	Bacteria - g-proteobacteria
+#prok:green sulfur bacteria	latest	Bacteria - green sulfur bacteria
+#prok:high GC Gram+	latest	Bacteria - high GC Gram+
+#prok:mycoplasmas	latest	Bacteria - mycoplasmas
+#prok:planctomycetes	latest	Bacteria - planctomycetes
+#prok:proteobacteria	latest	Bacteria - proteobacteria
+#prok:spirochetes	latest	Bacteria - spirochetes
+#prok:thermotogales	latest	Bacteria - thermotogales
+#prok:verrucomicrobia	latest	Bacteria - verrucomicrobia
+#fung:ascomycetes	latest	Fungi - ascomycetes
+#fung:basidiomycetes	latest	Fungi - basidiomycetes
+#fung:budding yeasts	latest	Fungi - budding yeasts
+#fung:chytrids	latest	Fungi - chytrids
+#fung:fungi	latest	Fungi - fungi
+#fung:microsporidians	latest	Fungi - microsporidians
+#plnt:green algae	latest	Plants (Viridiplantae) - green algae
+#plnt:mosses	latest	Plants (Viridiplantae) - mosses
+#plnt:plants	latest	Plants (Viridiplantae) - plants
+#prst:algae	latest	Protists (other Eukaryota) - algae
+#prst:alveolates	latest	Protists (other Eukaryota) - alveolates
+#prst:cellular slime molds	latest	Protists (other Eukaryota) - cellular slime molds
+#prst:cercozoans	latest	Protists (other Eukaryota) - cercozoans
+#prst:choanoflagellates	latest	Protists (other Eukaryota) - choanoflagellates
+#prst:euglenoids	latest	Protists (other Eukaryota) - euglenoids
+#prst:monads	latest	Protists (other Eukaryota) - monads
+#prst:protists	latest	Protists (other Eukaryota) - protists
+#prst:slime nets	latest	Protists (other Eukaryota) - slime nets
+#synt:synthetic	latest	Synthetic - synthetic
+#unkn:unknown	latest	Unknown / Unclassified
+#virs:eukaryotic viruses	latest	Virus - eukaryotic viruses
+#virs:prokaryotic viruses	latest	Virus - prokaryotic viruses
+#virs:viruses	latest	Virus - viruses
diff -r 000000000000 -r 3cdb96f2855d tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Fri Jan 12 22:11:39 2024 +0000
@@ -0,0 +1,17 @@
+<tables>
+    <!-- Location of NCBI FCS GX tool config -->
+    <table name="ncbi_fcs_gx_config" comment_char="#">
+        <columns>value, name, use_source_manifest, phone_home, phone_home_label, node_cache_dir</columns>
+        <file path="tool-data/ncbi_fcs_gx_config.tsv" />
+    </table>
+    <!-- Location of NCBI FCS GX databases -->
+    <table name="ncbi_fcs_gx_databases" comment_char="#">
+        <columns>value, source_manifest, name</columns>
+        <file path="tool-data/ncbi_fcs_gx_databases.loc" />
+    </table>
+    <!-- NCBI FCS GX divisions -->
+    <table name="ncbi_fcs_gx_divisions" comment_char="#">
+        <columns>value, tag, name</columns>
+        <file path="tool-data/ncbi_fcs_gx_divisions.tsv" />
+    </table>
+</tables>
diff -r 000000000000 -r 3cdb96f2855d tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Fri Jan 12 22:11:39 2024 +0000
@@ -0,0 +1,17 @@
+<tables>
+    <!-- Location of NCBI FCS GX tool config -->
+    <table name="ncbi_fcs_gx_config" comment_char="#">
+        <columns>value, name, use_source_manifest, phone_home, phone_home_label, node_cache_dir</columns>
+        <file path="${__HERE__}/test-data/ncbi_fcs_gx_config.tsv" />
+    </table>
+    <!-- Location of NCBI FCS GX databases -->
+    <table name="ncbi_fcs_gx_databases" comment_char="#">
+        <columns>value, source_manifest, name</columns>
+        <file path="${__HERE__}/test-data/ncbi_fcs_gx_databases.loc" />
+    </table>
+    <!-- NCBI FCS GX divisions -->
+    <table name="ncbi_fcs_gx_divisions" comment_char="#">
+        <columns>value, tag, name</columns>
+        <file path="${__HERE__}/test-data/ncbi_fcs_gx_divisions.tsv" />
+    </table>
+</tables>