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Changeset 0:28e95c6a944d (2019-01-16)

Next changeset 1:d9662c76b6d5 (2020-04-29)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc commit 665d364fb51576608b0eb66a4f89d92159925ccc

added:
taxonomy_filter_refseq.xml
test-data/all_fasta.loc
test-data/ncbi_taxonomy.loc
test-data/output1.fasta
test-data/sample_refseq.fasta
test-data/sample_tree_names.dmp
test-data/sample_tree_nodes.dmp
test-data/taxonomy/names.dmp
test-data/taxonomy/nodes.dmp
tool-data/all_fasta.loc.sample
tool-data/ncbi_taxonomy.loc.sample
tool_data_table_conf.xml.sample
tool_data_table_conf.xml.test

diff -r 000000000000 -r 28e95c6a944d taxonomy_filter_refseq.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/taxonomy_filter_refseq.xml Wed Jan 16 08:30:47 2019 -0500

[

@@ -0,0 +1,117 @@
+<tool id="taxonomy_filter_refseq" name="Filter RefSeq by taxonomy" version="@TOOL_VERSION@+galaxy0">
+    <description>Only retain sequences that are descendants of a given taxonomic node.</description>
+    <macros>
+        <token name="@TOOL_VERSION@">0.1.4</token>
+    </macros>
+    <edam_topics>
+        <edam_topic>topic_0091</edam_topic>
+    </edam_topics>
+    <edam_operations>
+        <edam_operation>operation_3460</edam_operation>
+    </edam_operations>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">rust-ncbitaxonomy</requirement>
+    </requirements>
+    
+    <command detect_errors="aggressive"><![CDATA[
+        #if str($refseq.refseq_source) == 'cached':
+            #set $refseq_input = str( $refseq.cached_refseq.fields.path )
+        #else:
+            ln -s '$refseq.history_refseq' refseq.fasta &&
+            #set $refseq_input = "refseq.fasta"
+        #end if
+        #if str($taxonomy.taxonomy_source) == 'cached':
+            #set $taxonomy_dir = $taxonomy.taxonomy_table.fields.path
+        #else:
+            mkdir taxonomy && ln -s '$taxonomy.nodes' taxonomy/nodes.dmp && ln -s '$taxonomy.names' taxonomy/names.dmp &&
+            #set $taxonomy_dir = 'taxonomy'
+        #end if
+     taxonomy_filter_refseq '$refseq_input' '$taxonomy_dir' '$ancestor_name' >'$refseq_output_fasta'
+    ]]></command>
+    <inputs>
+        <conditional name="taxonomy">
+            <param name="taxonomy_source" type="select" label="Choose source of NCBI Taxonomy">
+                <option value="cached" selected="true">Use built-in NCBI Taxonomy database</option>
+                <option value="history">Datasets from history</option>
+            </param>
+            <when value="cached">
+                <param type="select" name="taxonomy_table" label="NCBI Taxonomy database">
+                    <options from_data_table="ncbi_taxonomy">
+                        <filter type="sort_by" column="name" />
+                        <validator type="no_options" message="No NCBI Taxonomy downloads are available" />
+                    </options>
+                    <validator type="no_options" message="No NCBI Taxonomy database download is available" />
+                </param>
+            </when>
+            <when value="history">
+                <param name="nodes" type="data" format="txt" label="NCBI Taxonomy nodes.dmp file" />
+                <param name="names" type="data" format="txt" label="NCBI Taxonomy names.dmp file" />
+            </when>
+        </conditional>
+        <conditional name="refseq">
+            <param name="refseq_source" type="select" label="Choose source of RefSeq sequences">
+                <option value="cached" selected="true">Use a built-in RefSeq FASTA file</option>
+                <option value="history">History</option>
+            </param>
+            <when value="cached">
+                <param type="select" name="cached_refseq" label="Select RefSeq FASTA file">
+                    <options from_data_table="all_fasta">
+                        <filter type="sort_by" column="name" />
+                        <validator type="no_options" message="No FASTA data is available" />
+                    </options>
+                    <validator type="no_options" message="No FASTA data is available" />
+                </param>
+            </when>
+            <when value="history">
+                <param type="data" name="history_refseq" format="fasta" label="RefSeq FASTA file" />
+            </when>
+        </conditional>
+        <param name="ancestor_name" type="text" label="Ancestor taxon (scientific) name" />
+    </inputs>
+    <outputs>
+        <data name="refseq_output_fasta" format="fasta" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="taxonomy_source" value="history" />
+            <param name="refseq_source" value="history" />
+            <param name="nodes" ftype="txt" value="sample_tree_nodes.dmp" />
+            <param name="names" ftype="txt" value="sample_tree_names.dmp" />
+            <param name="history_refseq" ftype="fasta" value="sample_refseq.fasta" />
+            <param name="ancestor_name" value="unclassified bacterial viruses" />
+            <output name="refseq_output_fasta" value="output1.fasta" />
+        </test>
+        <test>
+            <param name="taxonomy_source" value="cached" />
+            <param name="taxonomy_table" value="2019-01-01" />
+            <param name="refseq_source" value="cached" />
+            <param name="cached_refseq" value="refseq_sample" />
+            <param name="nodes" ftype="txt" value="sample_tree_nodes.dmp" />
+            <param name="names" ftype="txt" value="sample_tree_names.dmp" />
+            <param name="history_refseq" ftype="fasta" value="sample_refseq.fasta" />
+            <param name="ancestor_name" value="unclassified bacterial viruses" />
+            <output name="refseq_output_fasta" value="output1.fasta" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        This tool allows NCBI RefSeq sequences to be filtered so that only those whose species name are
+        descendants of a given taxon in the NCBI taxonomy are retained. For example, from the NCBI RefSeq
+        "other vertebrate" file only ray finned fishes can be retained by filtering for "Actinopterygii".
+
+        The NCBI RefSeq FASTA files can either be provided by the Galaxy administrator or from the user
+        history. The NCBI taxonomy should be provided by the Galaxy administrator but if that is not
+        possible the nodes.dmp and names.dmp files from the NCBI taxonomy can be provided in the history.
+    ]]></help>
+    <citations>
+       <citation type="bibtex">
+    @misc{vanHeusden2019,
+    author = {van Heusden, Peter},
+    year = {2019},
+    title = ncbitaxonomy Rust crate},
+    publisher = {crates.io},
+    journal = {Rust Package Registry},
+    url = {https://crates.io/crates/ncbitaxonomy},
+    }
+        </citation>
+    </citations>
+</tool>

diff -r 000000000000 -r 28e95c6a944d test-data/all_fasta.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc Wed Jan 16 08:30:47 2019 -0500

@@ -0,0 +1,1 @@
+refseq_sample refseq_sample RefSeq viral sample ${__HERE__}/sample_refseq.fasta
\ No newline at end of file

diff -r 000000000000 -r 28e95c6a944d test-data/ncbi_taxonomy.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ncbi_taxonomy.loc Wed Jan 16 08:30:47 2019 -0500

@@ -0,0 +1,1 @@
+2019-01-01 2019-01-01 ${__HERE__}/taxonomy
\ No newline at end of file

diff -r 000000000000 -r 28e95c6a944d test-data/output1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output1.fasta Wed Jan 16 08:30:47 2019 -0500

[

@@ -0,0 +1,27 @@
+>YP_009173773.1 putative ATP-dependent DNA helicase [Mycoplasma phage phiMFV1]
+MNKMPWESEEVEYKKSTSELKEAIISLTAMLNKKGTGTVYFGVKDDRTVVGLEIGNKTMRDISQAISNNVKPEIMPRISI
+EFIDNQNVIKVEAEGEQKPYSAYDKYYIRIGEEDKKLNRDKLVDFVQKSVSKINICEIENKDQDLTFNSFLLYANIKNLT
+VNKDTFEKNFDLKTKNNKYNLMSYLLADNNDISIKVNTFKDNDKSVLLKRNEYGNKCLFYAIESVLNYVGSINDTYVDLS
+TATRSEQKLFNFECFREAWLNACIHNRWDEKYPPQVNIFKDYIQIESNGGIPRNMTKEKFFKGVSRPVNEKLQKIFMQLD
+LVEQTGHGVPLIVKKYGEEAFEIDENTIWVKIPFNRKGFKRINEKENKNNLNDNQIKVIKTIEKESNITINQLSSTLSLS
+EGYIKKIINQLKNKNLIERNGLRKNGNWTIISYNL
+>YP_044791.1 RepB [Mycoplasma phage phiMFV1]
+MLLTTKQLQEFYKIEMENIAKNKSLLTNFNIIDNYANGLKPKQLYFLAARPGVGKTSFALNIIFNALENLKEDECIVLFS
+LEMDSIEIYSKLLALANSCSLKEVETNSKKIDFEDLNKKNLFIFDRYRNNFNNEKLSEVTPDIIYKSLNSIGLKIKAVFI
+DYFQLLDNQKYSSEREKLSQCSKQLKELSKIFNCNFFVLSQLSREYEKKTNNEPSFSDLKGTGSIEQDADLIMFLYNSSN
+NFNVGTLIPNKKTILNLSIAKNRNGELVKTNIDFIPHLAKFIES
+>YP_044792.1 hypothetical protein [Mycoplasma phage phiMFV1]
+MLNNKCDFCHKRFQPKKERYFWGNLVVCSEECLEQVSCYASEIDLNCEGENNE
+>YP_044793.1 hypothetical protein [Mycoplasma phage phiMFV1]
+MNKEKLIKFLIDLTEKENTKLKSDVKILKSKLKKIKKEYEEQEKAFDDLLKKL
+>YP_044794.1 hypothetical protein [Mycoplasma phage phiMFV1]
+MDIFKKMEIAEKDKIEKLLLNIDKFIWDCNSKGWTKSKNKKVISLYKKTLEEIKKNEKYDWLYVPIKSQIYKFADHDLKS
+DIFLWFSHTKILCGYTYLKDKWNF
+>YP_044795.1 MarRP [Mycoplasma phage phiMFV1]
+MKFLKEPPVFTEEQFKELVHYTDLEDNPTFEAYKSNAFFKIYSGAKGVSKSFSRMIETVYRLVNEKNFNSFWCRNQYNHI
+KGTLKPLLEKVLSFLAAKGLDYRPYISIYNTEAYWDYDDGGKGRAIFFGNWKNVQSFQGVTLSQKDFAWGELVIDEPIEK
+ELTEELEEIYKIQASNLEILIANTVLRSKNIEGFKTNVTFLYNIFTIDHFLIKDFHNPILPLYSGTDFLKKINLNLAKEL
+IENTYLQKEDLAFKEGMGIIVTMFSKYFVPKNELSDLQLKQFEALKTKDYKLWMITVAGFAFEEPPERYDYFMKSVLLNK
+KGNWDRKKCKIINIKQLETKLENEEICGLFYGFDYGLTDNCALVVVLLLSGARIIVLDIFEDIKKLLPKNKRRENKAIYN
+KVALIVKKWNEYFDKYNFKFYISWLLGNFDSFLYGDNVHSLQWMTEVFINNGINTKLLPASRFKGKKGFGIIDRQVWQKN
+IFENGLVELLPKAKSLLTLLCQQVIDKEDPKNPNQRNERINKKIYDVINAFEMANTLQNCEYRNYLFNKELKEKNEQNNY

diff -r 000000000000 -r 28e95c6a944d test-data/sample_refseq.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_refseq.fasta Wed Jan 16 08:30:47 2019 -0500

[

@@ -0,0 +1,54 @@
+>YP_009026408.1 Coat Protein [Arhar cryptic virus-II]
+MNQGDRVPPHADTPSAPVETPPPIQGPTTNDLSRATEFLVKSTRLCWLQTNHEKYRSYVTLNRNELYSTLVELYTHFFAS
+EWTTLRRYVEPYTTETIAHQQRFAARNYISGWFIDLYVSNREAVKKLTPLAYNEYYSTDKARHHPEYDNFLTLLSSAIRP
+THIMDTPEDTLYIPLIRRQRQLGTENNPFNITDFVYSYPFVCGLIQTLQARKCWKRSPLSDNTMGRATWLFDWHGDKMVA
+PFPATGNYTKDDVTMAYILGVPCTPLIGCVDVDDWQFIPPNVDINTVNPNTLVRIDDPRFPGAYSVRVIETQEEYYLPIS
+SEGAMEIASRLGRPQRPSKKRKTASASTSKDPTTPASSTMVEYSDDPVDFNAPGSVSKIIVITDYLFCR
+>YP_009137150.1 neurovirulence protein ICP34.5 [Human alphaherpesvirus 2]
+MSRRRGPRRRGPRRRPRPGAPAVPRPGAPAVPRPGALPTADSQMVPAYDSGTAVESAPAASSLLRRWLLVPQADDSDDAD
+YAGNDDAEWANSPPSEGGGKAPEAPHAAPAAACPPPPPRKERGPQRPLPPHLALRLRTTTEYLARLSLRRRRPPASPPAD
+APRGKVCFSPRVQVRHLVAWETAARLARRGSWARERADRDRFRRRVAAAEAVIGPCLEPEARARARARARAHEDGGPAEE
+EEAAAAARGSSAAAGPGRRAV
+>YP_009137151.1 ubiquitin E3 ligase ICP0 [Human alphaherpesvirus 2]
+MEPRPGTSSRADPGPERPPRQTPGTQPAAPHAWGMLNDMQWLASSDSEEETEVGISDDDLHRDSTSEAGSTDTEMFEAGL
+MDAATPPARPPAERQGSPTPADAQGSCGGGPVGEEEAEAGGGGDVCAVCTDEIAPPLRCQSFPCLHPFCIPCMKTWIPLR
+NTCPLCNTPVAYLIVGVTASGSFSTIPIVNDPRTRVEAEAAVRAGTAVDFIWTGNQRTAPRSLSLGGHTVRALSPTPPWP
+GTDDEDDDLADVDYVPPAPRRAPRRGGGGAGATRGTSQPAATRPAPPGAPRSSSSGGAPLRAGVGSGSGGGPAVAAVVPR
+VASLPPAAGGGRAQARRVGEDAAAAEGRTPPAGQPRAAQEPPIVISDSPPPSPRRPAGPGPLSFFSSSSAQVSSGPGGGG
+LPQSSGRAARPRAAVAPRVRSPPRAAAAPVVSASADAAGPAPPAVPVDAHRAPRSRMTQAQTDTQAQSLGRAGATDARGS
+GGPGAEGGPGVPRGTNTPGAAPHAAEGAAARPRKRRGSDSGPAASSSASSSAAPRSPLAPQGVGAKRAAPRRAPDSDSGD
+RGHGPLAPASAGAAPPSASPSSQAAVAAAASSSSSAASSSSSAASSSSSAASSSSSAASSSSAASSSSSSSSASSSAGGA
+GGSVASASGAGERRETSLGPRAAAPRGPRKCARKTRHAEGGPEPGARDPAPGLTRYLPIAGVSSVVALAPYVNKTVTGDC
+LPVLDMETGHIGAYVVLVDQTGNVADLLRAAAPAWSRRTLLPEHARNCVRPPDYPTPPASEWNSLWMTPVGNMLFDQGTL
+VGALDFHGLRSRHPWSREQGAPAPAGDAPAGHGE
+>YP_009137152.1 envelope glycoprotein L [Human alphaherpesvirus 2]
+MGFVCLFGLVVMGAWGAWGGSQATEYVLRSVIAKEVGDILRVPCMRTPADDVSWRYEAPSVIDYARIDGIFLRYHCPGLD
+TFLWDRHAQRAYLVNPFLFAAGFLEDLSHSVFPADTQETTTRRALYKEIRDALGSRKQAVSHAPVRAGCVNFDYSRTRRC
+VGRRDLRPANTTSTWEPPVSSDDEASSQSKPLATQPPVLALSNAPPRRVSPTRGRRRHTRLRRN
+>YP_009173773.1 putative ATP-dependent DNA helicase [Mycoplasma phage phiMFV1]
+MNKMPWESEEVEYKKSTSELKEAIISLTAMLNKKGTGTVYFGVKDDRTVVGLEIGNKTMRDISQAISNNVKPEIMPRISI
+EFIDNQNVIKVEAEGEQKPYSAYDKYYIRIGEEDKKLNRDKLVDFVQKSVSKINICEIENKDQDLTFNSFLLYANIKNLT
+VNKDTFEKNFDLKTKNNKYNLMSYLLADNNDISIKVNTFKDNDKSVLLKRNEYGNKCLFYAIESVLNYVGSINDTYVDLS
+TATRSEQKLFNFECFREAWLNACIHNRWDEKYPPQVNIFKDYIQIESNGGIPRNMTKEKFFKGVSRPVNEKLQKIFMQLD
+LVEQTGHGVPLIVKKYGEEAFEIDENTIWVKIPFNRKGFKRINEKENKNNLNDNQIKVIKTIEKESNITINQLSSTLSLS
+EGYIKKIINQLKNKNLIERNGLRKNGNWTIISYNL
+>YP_044791.1 RepB [Mycoplasma phage phiMFV1]
+MLLTTKQLQEFYKIEMENIAKNKSLLTNFNIIDNYANGLKPKQLYFLAARPGVGKTSFALNIIFNALENLKEDECIVLFS
+LEMDSIEIYSKLLALANSCSLKEVETNSKKIDFEDLNKKNLFIFDRYRNNFNNEKLSEVTPDIIYKSLNSIGLKIKAVFI
+DYFQLLDNQKYSSEREKLSQCSKQLKELSKIFNCNFFVLSQLSREYEKKTNNEPSFSDLKGTGSIEQDADLIMFLYNSSN
+NFNVGTLIPNKKTILNLSIAKNRNGELVKTNIDFIPHLAKFIES
+>YP_044792.1 hypothetical protein [Mycoplasma phage phiMFV1]
+MLNNKCDFCHKRFQPKKERYFWGNLVVCSEECLEQVSCYASEIDLNCEGENNE
+>YP_044793.1 hypothetical protein [Mycoplasma phage phiMFV1]
+MNKEKLIKFLIDLTEKENTKLKSDVKILKSKLKKIKKEYEEQEKAFDDLLKKL
+>YP_044794.1 hypothetical protein [Mycoplasma phage phiMFV1]
+MDIFKKMEIAEKDKIEKLLLNIDKFIWDCNSKGWTKSKNKKVISLYKKTLEEIKKNEKYDWLYVPIKSQIYKFADHDLKS
+DIFLWFSHTKILCGYTYLKDKWNF
+>YP_044795.1 MarRP [Mycoplasma phage phiMFV1]
+MKFLKEPPVFTEEQFKELVHYTDLEDNPTFEAYKSNAFFKIYSGAKGVSKSFSRMIETVYRLVNEKNFNSFWCRNQYNHI
+KGTLKPLLEKVLSFLAAKGLDYRPYISIYNTEAYWDYDDGGKGRAIFFGNWKNVQSFQGVTLSQKDFAWGELVIDEPIEK
+ELTEELEEIYKIQASNLEILIANTVLRSKNIEGFKTNVTFLYNIFTIDHFLIKDFHNPILPLYSGTDFLKKINLNLAKEL
+IENTYLQKEDLAFKEGMGIIVTMFSKYFVPKNELSDLQLKQFEALKTKDYKLWMITVAGFAFEEPPERYDYFMKSVLLNK
+KGNWDRKKCKIINIKQLETKLENEEICGLFYGFDYGLTDNCALVVVLLLSGARIIVLDIFEDIKKLLPKNKRRENKAIYN
+KVALIVKKWNEYFDKYNFKFYISWLLGNFDSFLYGDNVHSLQWMTEVFINNGINTKLLPASRFKGKKGFGIIDRQVWQKN
+IFENGLVELLPKAKSLLTLLCQQVIDKEDPKNPNQRNERINKKIYDVINAFEMANTLQNCEYRNYLFNKELKEKNEQNNY

diff -r 000000000000 -r 28e95c6a944d test-data/sample_tree_names.dmp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_tree_names.dmp Wed Jan 16 08:30:47 2019 -0500

b'@@ -0,0 +1,687 @@\n+1\t|\tall\t|\t\t|\tsynonym\t|\n+1\t|\troot\t|\t\t|\tscientific name\t|\n+10239\t|\tVira\t|\t\t|\tsynonym\t|\n+10239\t|\tViridae\t|\t\t|\tsynonym\t|\n+10239\t|\tViruses\t|\t\t|\tscientific name\t|\n+10239\t|\tviruses\t|\tviruses <blast10239>\t|\tblast name\t|\n+12333\t|\tbacterial virus\t|\tbacterial virus <unclassified bacterial viruses>\t|\tin-part\t|\n+12333\t|\tbacterial viruses\t|\tbacterial viruses <unclassified bacterial viruses>\t|\tin-part\t|\n+12333\t|\tprokaryotic virus\t|\tprokaryotic virus <unclassified bacterial viruses>\t|\tin-part\t|\n+12333\t|\tunclassified bacterial viruses\t|\t\t|\tscientific name\t|\n+12333\t|\tunclassified bacteriophages\t|\t\t|\tsynonym\t|\n+12333\t|\tunclassified phage\t|\t\t|\tsynonym\t|\n+12333\t|\tunclassified phages\t|\t\t|\tsynonym\t|\n+12340\t|\tBacteriophage 933J\t|\t\t|\tsynonym\t|\n+12340\t|\tColiphage 933J\t|\t\t|\tsynonym\t|\n+12340\t|\tEnterobacteria phage 933J\t|\t\t|\tscientific name\t|\n+12340\t|\tphage 933J\t|\t\t|\tsynonym\t|\n+12347\t|\tActinophage JHJ-1\t|\t\t|\tscientific name\t|\n+12347\t|\tBacteriophage JHJ-1\t|\t\t|\tsynonym\t|\n+12366\t|\tBacteriophage h4489a\t|\t\t|\tsynonym\t|\n+12366\t|\tStreptococcus pyogenes bacteriophage H4489A\t|\t\t|\tsynonym\t|\n+12366\t|\tStreptococcus pyogenes phage H4489A\t|\t\t|\tscientific name\t|\n+12371\t|\tBacteriophage h30\t|\t\t|\tsynonym\t|\n+12371\t|\tPhage h30\t|\t\t|\tscientific name\t|\n+12374\t|\tLactococcus bacteriophage\t|\t\t|\tsynonym\t|\n+12374\t|\tLactococcus phage\t|\t\t|\tscientific name\t|\n+12375\t|\tLactococcus 1 bacteriophage\t|\t\t|\tsynonym\t|\n+12375\t|\tLactococcus bacteriophage (ISOLATE 7-9)\t|\t\t|\tsynonym\t|\n+12375\t|\tLactococcus phage (ISOLATE 7-9)\t|\t\t|\tscientific name\t|\n+12386\t|\tLactococcus phage mi7-9\t|\t\t|\tscientific name\t|\n+12388\t|\tMycobacterium phage FRAT1\t|\t\t|\tscientific name\t|\n+12388\t|\tmycobacteriophage FRAT1\t|\t\t|\tsynonym\t|\n+12392\t|\tBacteriophage mv4\t|\t\t|\tsynonym\t|\n+12392\t|\tLactobacillus delbrueckii subsp. bulgaricus phage mv4\t|\t\t|\tsynonym\t|\n+12392\t|\tLactobacillus phage mv4\t|\t\t|\tscientific name\t|\n+12392\t|\tLactococcus delbrueckii bacteriophage MV4\t|\t\t|\tsynonym\t|\n+12392\t|\tphage mv4\t|\t\t|\tsynonym\t|\n+12403\t|\tBacteriophage P32\t|\t\t|\tsynonym\t|\n+12403\t|\tLeuconostoc oenos phage P32\t|\t\t|\tsynonym\t|\n+12403\t|\tLeuconostoc phage P32\t|\t\t|\tscientific name\t|\n+12404\t|\tBacteriophage P37\t|\t\t|\tsynonym\t|\n+12404\t|\tLeuconostoc oenos phage P37\t|\t\t|\tsynonym\t|\n+12404\t|\tLeuconostoc phage P37\t|\t\t|\tscientific name\t|\n+12405\t|\tBacteriophage P54\t|\t\t|\tsynonym\t|\n+12405\t|\tLeuconostoc oenos phage P54\t|\t\t|\tsynonym\t|\n+12405\t|\tLeuconostoc phage P54\t|\t\t|\tscientific name\t|\n+12406\t|\tBacteriophage PAt5-12\t|\t\t|\tsynonym\t|\n+12406\t|\tLeuconostoc oenos phage PAt5-12\t|\t\t|\tsynonym\t|\n+12406\t|\tLeuconostocphage PAt5-12\t|\t\t|\tscientific name\t|\n+12408\t|\tBacteriophage PZt11-15\t|\t\t|\tsynonym\t|\n+12408\t|\tLeuconostoc oenos phage PZt11-15\t|\t\t|\tsynonym\t|\n+12408\t|\tLeuconostoc phage PZt11-15\t|\t\t|\tscientific name\t|\n+12409\t|\tBacteriophage d-16 phi\t|\t\t|\tsynonym\t|\n+12409\t|\tClostridium phage d-16 phi\t|\t\t|\tscientific name\t|\n+12412\t|\tStaphylococcus aureus bacteriophage phi-42\t|\t\t|\tsynonym\t|\n+12412\t|\tStaphylococcus aureus phage phi-42\t|\t\t|\tsynonym\t|\n+12412\t|\tStaphylococcus phage phi-42\t|\t\t|\tscientific name\t|\n+12412\t|\tbacteriophage phi 42\t|\t\t|\tsynonym\t|\n+12412\t|\tbacteriophage phi-42\t|\t\t|\tsynonym\t|\n+12413\t|\tBacteriophage phi 7-9\t|\t\t|\tsynonym\t|\n+12413\t|\tLactococcusphage phi7-9\t|\t\t|\tscientific name\t|\n+12420\t|\tFilamentous bacteriophage\t|\t\t|\tsynonym\t|\n+12420\t|\tFilamentous phage\t|\t\t|\tscientific name\t|\n+12424\t|\tBacteriophage 13\t|\t\t|\tsynonym\t|\n+12424\t|\tPhage 13\t|\t\t|\tscientific name\t|\n+12425\t|\tBacteriophage 16\t|\t\t|\tsynonym\t|\n+12425\t|\tPhage 16\t|\t\t|\tscientific name\t|\n+12427\t|\tLactococcus lactis phage phi 197\t|\t\t|\tscientific name\t|\n+12427\t|\tphage phi 197\t|\t\t|\tsynonym\t|\n+12427\t|\tphage phi-197\t|\t\t|\tsynonym\t|\n+12428\t|\tRetronphage phi R73\t|\t\t|\tscientific name\t|\n+28368\t|\tCorynebacterium diphtheriae phage\t|\t\t|\tscientific name\t|\n+28368\t|\tCorynebacterium diphtheriae virus\t|\t\t|\tsynonym\t|\n+31760\t|\tColitis phage\t|\t\t|\tscientific name\t|\n+33768\t|\tBacteriophage L10\t|\t\t|\tsynonym\t|\n+33768\t|\tLeuconostoc oenos bacteriophage L10\t|\t\t|\tsynonym\t|\n+33768\t|\tLeuconostoc oenos phage L10\t|\t\t|\tsynonym\t|\n+33768\t|\tLe'..b'|\tNovosphingobium phage N-AFCa0802-57\t|\t\t|\tscientific name\t|\n+458443\t|\tNovosphingobium phage N-AFCa0802-24\t|\t\t|\tscientific name\t|\n+458444\t|\tNovosphingobium phage N-AFNF0810-25\t|\t\t|\tscientific name\t|\n+458445\t|\tNovosphingobium phage N-AFCF0810-26\t|\t\t|\tscientific name\t|\n+458446\t|\tNovosphingobium phage N-AFCM0810-27\t|\t\t|\tscientific name\t|\n+458447\t|\tNovosphingobium phage N-AFCM0810-28\t|\t\t|\tscientific name\t|\n+458448\t|\tNovosphingobium phage N-AFCa0810-29\t|\t\t|\tscientific name\t|\n+458449\t|\tNovosphingobium phage N-AFCa0810-30\t|\t\t|\tscientific name\t|\n+458450\t|\tNovosphingobium phage N-AFNF0824-31\t|\t\t|\tscientific name\t|\n+458451\t|\tNovosphingobium phage N-AFCF0824-32\t|\t\t|\tscientific name\t|\n+458452\t|\tNovosphingobium phage N-AFCM0824-33\t|\t\t|\tscientific name\t|\n+458453\t|\tNovosphingobium phage N-AFCa0824-34\t|\t\t|\tscientific name\t|\n+458454\t|\tNovosphingobium phage N-AFCa0824-35\t|\t\t|\tscientific name\t|\n+458455\t|\tNovosphingobium phage N-AFCa0824-36\t|\t\t|\tscientific name\t|\n+458456\t|\tNovosphingobium phage N-AFCF0901-37\t|\t\t|\tscientific name\t|\n+458457\t|\tNovosphingobium phage N-AFCM0901-40\t|\t\t|\tscientific name\t|\n+458458\t|\tNovosphingobium phage N-AFCa0901-41\t|\t\t|\tscientific name\t|\n+458459\t|\tNovosphingobium phage N-AFCa0901-42\t|\t\t|\tscientific name\t|\n+458460\t|\tNovosphingobium phage N-AFNF0913-43\t|\t\t|\tscientific name\t|\n+458461\t|\tNovosphingobium phage N-AFCM0913-47\t|\t\t|\tscientific name\t|\n+458462\t|\tNovosphingobium phage N-AFCF0714-51\t|\t\t|\tscientific name\t|\n+458463\t|\tNovosphingobium phage N-AFCM0714-52\t|\t\t|\tscientific name\t|\n+458464\t|\tNovosphingobium phage N-AFNF0922-55\t|\t\t|\tscientific name\t|\n+458465\t|\tSphingomonas phage S-AFNF0615-61\t|\t\t|\tscientific name\t|\n+458466\t|\tSphingomonas phage S-AFCF0802-69\t|\t\t|\tscientific name\t|\n+458467\t|\tSphingomonas phage S-AFNF0810-70\t|\t\t|\tscientific name\t|\n+458468\t|\tSphingomonas phage S-AFCa0824-71\t|\t\t|\tscientific name\t|\n+458469\t|\tSphingomonas phage S-AFCa0901-72\t|\t\t|\tscientific name\t|\n+458470\t|\tNovosphingobium phage N-AFCa0707-83\t|\t\t|\tscientific name\t|\n+458471\t|\tNovosphingobium phage N-AFCa0714-84\t|\t\t|\tscientific name\t|\n+458472\t|\tNovosphingobium phage N-AFCa0802-85\t|\t\t|\tscientific name\t|\n+458473\t|\tNovosphingobium phage N-AFCM0802-86\t|\t\t|\tscientific name\t|\n+458474\t|\tNovosphingobium phage N-AFCF0901-89\t|\t\t|\tscientific name\t|\n+458475\t|\tNovosphingobium phage N-AFCa0901-90\t|\t\t|\tscientific name\t|\n+458476\t|\tNovosphingobium phage N-AFCM0901-91\t|\t\t|\tscientific name\t|\n+458477\t|\tNovosphingobium phage N-An-FWCa0913-92\t|\t\t|\tscientific name\t|\n+462299\t|\tEnterobacteria phage VT1-Sakai\t|\t\t|\tscientific name\t|\n+464033\t|\tCampylobacter phage CGC-2007\t|\t\t|\tscientific name\t|\n+472964\t|\tStreptococcus phage NZ131.1\t|\t\t|\tscientific name\t|\n+472965\t|\tStreptococcus phage NZ131.2\t|\t\t|\tscientific name\t|\n+472966\t|\tStreptococcus phage NZ131.3\t|\t\t|\tscientific name\t|\n+483783\t|\tBacillus phage bg1\t|\t\t|\tscientific name\t|\n+483784\t|\tBacillus phage bg2\t|\t\t|\tscientific name\t|\n+483785\t|\tBacillus phage bg3\t|\t\t|\tscientific name\t|\n+498338\t|\tSynechococcus phage SPGM99-02\t|\t\t|\tscientific name\t|\n+498339\t|\tSynechococcus phage SPGM99-07\t|\t\t|\tscientific name\t|\n+498340\t|\tSynechococcus phage SPGM99-10\t|\t\t|\tscientific name\t|\n+498341\t|\tSynechococcus phage SPGM99-12\t|\t\t|\tscientific name\t|\n+498342\t|\tSynechococcus phage SPGM99-14\t|\t\t|\tscientific name\t|\n+498343\t|\tSynechococcus phage SPGM99-15\t|\t\t|\tscientific name\t|\n+498344\t|\tSynechococcus phage SPGM99-16\t|\t\t|\tscientific name\t|\n+498345\t|\tSynechococcus phage SPGM99-20\t|\t\t|\tscientific name\t|\n+498346\t|\tSynechococcus phage SPGM99-21\t|\t\t|\tscientific name\t|\n+498347\t|\tSynechococcus phage SPGM99-24\t|\t\t|\tscientific name\t|\n+498348\t|\tSynechococcus phage SPGM99-27\t|\t\t|\tscientific name\t|\n+498349\t|\tSynechococcus phage SPGM99-28\t|\t\t|\tscientific name\t|\n+498350\t|\tSynechococcus phage SPGM99-29\t|\t\t|\tscientific name\t|\n+498351\t|\tSynechococcus phage SPGM99-30\t|\t\t|\tscientific name\t|\n+498352\t|\tSynechococcus phage SPGM99-31\t|\t\t|\tscientific name\t|\n+498353\t|\tSynechococcus phage SPGM99-39\t|\t\t|\tscientific name\t|\n+504556\t|\tPropionibacterium phage PAS7\t|\t\t|\tscientific name\t|\n'

diff -r 000000000000 -r 28e95c6a944d test-data/sample_tree_nodes.dmp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sample_tree_nodes.dmp Wed Jan 16 08:30:47 2019 -0500

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diff -r 000000000000 -r 28e95c6a944d test-data/taxonomy/names.dmp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/taxonomy/names.dmp Wed Jan 16 08:30:47 2019 -0500

diff -r 000000000000 -r 28e95c6a944d test-data/taxonomy/nodes.dmp
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/taxonomy/nodes.dmp Wed Jan 16 08:30:47 2019 -0500

diff -r 000000000000 -r 28e95c6a944d tool-data/all_fasta.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample Wed Jan 16 08:30:47 2019 -0500

@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id> <dbkey> <display_name> <file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
+#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#

diff -r 000000000000 -r 28e95c6a944d tool-data/ncbi_taxonomy.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/ncbi_taxonomy.loc.sample Wed Jan 16 08:30:47 2019 -0500

@@ -0,0 +1,2 @@
+#value name path
+#2018-12-01 2018-12-01 /opt/galaxy/tool-data/ncbi_taxonomy/2018-12-01
\ No newline at end of file

diff -r 000000000000 -r 28e95c6a944d tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Wed Jan 16 08:30:47 2019 -0500

@@ -0,0 +1,12 @@
+<tables>
+    
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+    
+    <table name="ncbi_taxonomy" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/ncbi_taxonomy.loc" />
+    </table>
+</tables>
\ No newline at end of file

diff -r 000000000000 -r 28e95c6a944d tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Wed Jan 16 08:30:47 2019 -0500

@@ -0,0 +1,12 @@
+<tables>
+    
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/all_fasta.loc" />
+    </table>
+    
+    <table name="ncbi_taxonomy" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/ncbi_taxonomy.loc" />
+    </table>
+</tables>
\ No newline at end of file