| Next changeset 1:e12dacb1d3b1 (2025-04-16) |
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Commit message:
planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 3c8e23e1dea22f625fb6f77ae61e1f4b605aaae2 |
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added:
macros.xml phatyp.xml test-data.sh test-data/example_contigs.fa test-data/phabox.loc tool-data/phabox.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r eb22ba00cd4c macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Nov 12 09:32:16 2024 +0000 |
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| b'@@ -0,0 +1,207 @@\n+<macros>\n+ <token name="@TOOL_VERSION@">2.1.5</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1093/bioadv/vbad101</citation>\n+ <yield/>\n+ </citations>\n+ </xml>\n+\n+ <xml name="general">\n+ <param argument="--dbdir" type="select" label="Phabox2 database">\n+ <options from_data_table="phabox"/>\n+ </param>\n+ <param argument="--contigs" type="data" format="fasta" optional="false" label="Contig sequences"/>\n+ <param argument="--proteins" type="data" format="fasta" optional="true" label="Predicted proteins"/>\n+ <param argument="--len" type="integer" value="3000" min="0" label="Minimum contig length" help="Contigs with length smaller than this value will not proceed"/>\n+ </xml>\n+ <token name="@GENERAL@"><![CDATA[\n+ --dbdir \'$dbdir.fields.path\'\n+ --outpth output/ \n+ --contigs \'$contigs\'\n+ #if $proteins\n+ --proteins \'$proteins\'\n+ #end if\n+ --midfolder intermediate/\n+ --len $len\n+ --threads "\\${GALAXY_SLOTS:-1}"\n+ ]]></token>\n+\n+\n+ <xml name="phamer">\n+ <section name="phamer" title="Options for virus identification" help="">\n+ <param argument="--reject" type="float" value="10" min="0" max="20" label="Minimum known proteins percentage" help="Reject sequences in which the percent proteins aligned to known phages is smaller than the value"/>\n+ </section>\n+ </xml>\n+ <token name="@PHAMER@"><![CDATA[\n+ --reject $phamer.reject\n+ ]]></token>\n+\n+\n+ <xml name="network">\n+ <section name="network" title="Options for virus-virus connections" help="The options below are used to generate a network for virus-virus connections. The current parameters are optimized for the ICTV 2024 and are highly accurate for grouping genus-level vOTUs. When making changes, make sure you understand what they are.">\n+ <param argument="--aai" type="float" value="75" min="0" max="100" label="Average amino acids identity"/>\n+ <param argument="--share" type="float" value="15" min="0" max="100" label="Minimum shared number of proteins"/>\n+ <param argument="--pcov" type="float" value="80" min="0" max="100" label="Protein-based coverage"/>\n+ <!-- \\-\\-draw not recommended top be used according to CLI help -->\n+ </section>\n+ </xml>\n+ <token name="@NETWORK@"><![CDATA[\n+ --aai $network.aai\n+ --share $network.share\n+ --pcov $network.pcov\n+ ]]></token>\n+\n+ <xml name="crispr">\n+ <section name="crispr" title="Options used to predict CRISPRs based on MAGs" help="">\n+ <param argument="--bfolder" type="data" format="true" optional="true" label="MAGS"/>\n+ <param argument="--cpident" type="float" value="90" min="90" max="100" label="Alignment identity for CRISPRs"/>\n+ <param argument="--ccov" type="float" value="90" min="0" max="100" label="Alignment coverage for CRISPRs"/>\n+ <param argument="--blast" type="select" label="BLAST program for CRISPRs" help="blastn-short will lead to more sensitive results but require more time to execute the program">\n+ <option value="blastn">blastn</option>\n+ <option value="blastn-short">blastn-short</option>\n+ </param>\n+ </section>\n+ </xml>\n+ <token name="@CRISPR_PRE@"><![CDATA[\n+ #if $crispr.bfolder\n+ mkdir bfolder &&\n+ #for b in $crispr.bfolder\n+ #set bname = re.sub(\'[^\\w\\-_\\.]\', \'_\', $b.element_identifier)\n+ ln -s \'$b\' \'$bname\' &&\n+ #end for\n+ #end if\n+ ]]></token>\n+ <token name="@CRISPR@"><![CDATA[\n+ #if $crispr.bfolder\n+ --bfolder bfolder\n+ #end if\n+ --cpident $crispr.cpident\n+ --ccov $c'..b'ption>\n+ <option value="terl" selected="true">terminase large subunit (92)</option>\n+ </param>\n+ <param argument="--mcov" type="float" value="50" min="0" max="100" label="Alignment coverage for matching marker genes"/>\n+ <param argument="--mpident" type="float" value="25" min="0" max="100" label="Alignment identitiy for matching marker genes"/>\n+ </section>\n+ </xml>\n+ <token name="@TREE@"><![CDATA[\n+ --marker \n+ #for m in $tree.marker\n+ $m\n+ #end for\n+ --mcov $tree.mcov\n+ --mpident $tree.mpident\n+ ## constructing the MSA and building the tree\n+ ## (the program would use mafft and fasttree)\n+ ## can be done more flexibly in Galaxy\n+ ## (leavinh this here to ensure it won\'t be implemented)\n+ ## --msa Y\n+ ## --tree Y\n+ ]]></token>\n+\n+ <xml name="supp_out" tokens="task">\n+ <collection name="@TASK@_supp_out" type="list" label="${tool.name} on ${on_string}: @TASK@ supplement">\n+ <discover_datasets pattern="(?P<designation>.+).fa" format="fasta" directory="output/final_prediction/@TASK@_supplementary"/>\n+ <discover_datasets pattern="(?P<designation>.+).tsv" format="tabular" directory="output/final_prediction/@TASK@_supplementary"/>\n+ <discover_datasets pattern="(?P<designation>.+).tab" format="tabular" directory="output/final_prediction/@TASK@_supplementary"/>\n+ <filter>supplements and "@TASK@" in supplements</filter>\n+ </collection>\n+ </xml>\n+\n+ <token name="@COMMON_OUTPUT_DOC@"><![CDATA[\n+A tabular dataset with the following columns:\n+\n+- Accession: the accession or the name of the input contigs.\n+- Length: the length of input contigs.\n+ ]]></token>\n+ <token name="@PHAMER_OUTPUT_DOC@"><![CDATA[\n+- Pred: virus or non-virus.\n+- Proportion: the proportion of the proteins that can be aligned to the virus database (from 0 to 1).\n+- PhaMerScore: the prediction score given by the deep learning model.\n+- PhaMerConfidence: the confidence of prediction, determined by both Proportion and PhaMerScore (high-confidence, medium-confidence, low-confidence, lower than reject threshold (according to the --reject parameter, default: 0.1)).\n+ For the virus with low-confidence or lower than reject threshold, we recommend you to run the contamination task to check their sequence quality.\n+ ]]></token>\n+ <token name="@PHAGCN_OUTPUT_DOC@"><![CDATA[\n+- Lineage: the predicted taxonomy lineage (NCBI version) of the contigs. Each rank is separated by the \';\'.\n+- PhaGCNScore: the predicted score for each rank in the lineage. Each rank is separated by the \';\'.\n+- Genus: whether the contig has a genus level name (\'-\' means unknown).\n+- GenusCluster: if the Genus is \'-\', the program will assign a genus-level grouping result: group_idx (idx = 1, 2, 3, ...) or singleton. This can be viewed as genus-level OTUs based on the average shared protein identities between sequences.\n+ ]]></token>\n+ <token name="@PHATYP_OUTPUT_DOC@"><![CDATA[\n+- TYPE: virulent or temperate (virus).\n+- PhaTYPScore: the prediction score given by the deep learning model.\n+ ]]></token>\n+ <token name="@CHERRY_OUTPUT_DOC@"><![CDATA[\n+- Host: the predicted host (NCBI taxonomy) of the contigs. \'-\' means unknown host.\n+- CHERRYScore: the predicted score from the model.\n+- Method:\n+ - CRISPR-based(MAG): CRISPRs alignment results from provided MAG (if any)\n+ - CRISPR-based(DB): CRISPRs alignment results from database.\n+ - AAI-based: predicting host based on virus-simil\n+- Host_NCBI_lineage\n+- Host_GTDB_lineage\n+ ]]></token>\n+\n+ <token name="@COMMON_INPUT_DOC@"><![CDATA[\n+**Input**\n+\n+- Contig sequences in FASTA format\n+- Optionally own predicted protein sequences can be given (by default the tool will use prodigal and diamond blastp for the prediction)\n+ ]]></token>\n+\n+</macros>\n' |
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| diff -r 000000000000 -r eb22ba00cd4c phatyp.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phatyp.xml Tue Nov 12 09:32:16 2024 +0000 |
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| @@ -0,0 +1,49 @@ +<tool id="phabox_phatyp" name="PhaBOX phatyp" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1" license="MIT"> + <description>Lifestyle prediction</description> + <macros> + <import>macros.xml</import> + </macros> + <xrefs> + <xref type="bio.tools">phabox</xref> + </xrefs> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">phabox</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + phabox2 --task phatyp + @GENERAL@ + ]]></command> + <inputs> + <expand macro="general"/> + </inputs> + <outputs> + <data name="out" format="tabular" from_work_dir="output/final_prediction/phatyp_prediction.tsv"/> + </outputs> + <tests> + <test> + <param name="dbdir" value="phaboxdb"/> + <param name="contigs" value="example_contigs.fa"/> + <output name="out"> + <assert_contents> + <has_line line="Accession	Length	TYPE	PhaTYPScore"/> + <has_n_lines n="11"/> + <has_n_columns n="4"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +Classify the lifestyles of phages. + + +@COMMON_INPUT_DOC@ + +**Output**: + +@COMMON_OUTPUT_DOC@ +@PHATYP_OUTPUT_DOC@ + ]]></help> + <expand macro="citations"> + <citation type="doi">10.1093/bib/bbac487</citation> + </expand> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r eb22ba00cd4c test-data.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data.sh Tue Nov 12 09:32:16 2024 +0000 |
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| @@ -0,0 +1,6 @@ +#!/bin/bash + +wget https://github.com/KennthShang/PhaBOX/releases/download/v2/phabox_db_v2.zip +unzip phabox_db_v2.zip +rm phabox_db_v2.zip +mv phabox_db_v2/ test-data/ |
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| diff -r 000000000000 -r eb22ba00cd4c test-data/example_contigs.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example_contigs.fa Tue Nov 12 09:32:16 2024 +0000 |
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| b'@@ -0,0 +1,20 @@\n+>example_0\n+AGATACTAACTCTGCTGCATAGACAAGAAATTCGTCTTTGCGGGAATATTTACCTGCAAGGTATATTTTCACATTAACCTCTCAAAAAGCGTTTAACCACTGCTGGTACAACCCCATTTCCACAGGCTCTAATCCTGTCCAACCGATTGGCAACCCTTGCAGCCACTCGACCCAGTCCGGGTTCAGTTGACCACCAACCACATTCGGTAACTGGAAATTTCTGCTTGATGGGCCTTTCCAATCCCTCGCTATTGGCGTTGGTAACCTCTCCATTGCCGTCGCCAGCCCATCCCCGCTGTTCTTGCTGGCACCTTTCCGATTGTAGTTGCCATCTACTGTTGGCGTCGGCCACTGCACCCGCTTGACTACCTGTGACAGATTTGAGCATCCGCCCTTCTTCTTCCGTGCCAAGAGATTCCCGTCTGGGATATCGTATGCATCCATTGCTTGAGGGGTAGGCCACATCCCCGTTTTTGCCATCGCTCCCAGGCTGTTGATGCCGCCCCATCTTTTCGTATTCGAGTTCTTGTTCGGCGCATCTACTGCCATTGGCGTAGGCAAGACACCACCAGCGCCAACGCAGGTGTGGCGCGCCAACTGCCGCAGCCGGTACGCAGTCCCAGACGCAGTCATACCCGATCTGGGAAAGCTGCCCGACCACGGTTCCCCCATACCCGTTAGCAAGGATGCCTGGAACGTTCTCCAGCAAGACGTACCCTGGTCCCACATCCCGAATGACTCTAAGGGTTTCCGGCCACAGATTACGCTCGTCACTAGCTCCTCGGCGTTTACCCGCTGTGCTGTGGGGCTGGCAGGGGAAACCTGCCGTAATAATCTCCACCAGTCCTCTACACTGCTTACCATCGAAGGTACGTATATCGGGCCAGATTGGGGCATCGTCAAGGAGTCCATCCCTAATCCTTGCTTTGATGATTTCCTGGCAGTACGGCTCTATTTCCACATAACCGATGGTACGTATGGATAAGCCCGCTAGCCGCAACCCTAGTGTAAAACCACAGTAGCCAGAGAAGAGGCTAAGCTCGTTCATAAAAGCCTCAACTGCCCCTTCTGGATTACCGCATCTTCAAGATTTTTGCGGGCTGTATTAAAATATTCAGGTTTCAATTCGATTCCCAGGAACTTCCTGTTTTGCAGGATTGCCACATACCCTTCGCTGCCAATCCCCATAAAGGGGCTGAGTACCAGCTCGCCAGGATTGCTCCACAGCCTGATACACCGCTCAATCAAGCTTAATTGTAGCGGGCAAATATGCCGCTCATCCCTATCAGTGCGTGCTACCTGTGTATTAAGGGTATCTGTTTCCCTAATATCTAGCCACACAGGATGCGCCCAGGTTATCCAGTCTTCATTAGTTATATCCGGATGTATTGGCACAGCATTTTCCCCAGGCTTACGGAACACCAGAATGTAATCAGCCAGCCCAGGTCTGAGCCATGATGCATCTTTTTTAAGCTGAGCAAAAAGCAGCGCCTTGCTATGAGTACGTACAGCTTGCGCCTGGGGATTCTTTCCCACCGTGATATCCCCGTGGTAATGGAAACCACCTCGTATAAAAGCATCAATCACCTTGCCCCGAAAATCCTTGAGACCAATAAAGCCATCATGGGCTAGAGTAGATGATACTTGAGCAACATGAACAGCAGCGATACGTCCAGTCTTTGTCACCCGATGTAACTCTTTTATCATAAAATTGAAATGTTCGAAGAATTCGGCTTCATCCTTAGAATTGCCCATATCTCGCTCAGAATCACTGTATACGAATAATGACATAAACGGTGGCGAGAACACCGAGAAATCAACCGACTCGGTGCTAACCTCAGCTAGCCTCTCGACACAATCGCCAAGCATCAAGGTGTAACCATCGCCAGTGGCTATGTCCGTGTGGTACCCATTGGATTCCAACTTGACTAGCCCCAATTCCTCCTTCTCATACTCAGCAACATTGGCTACCAGGTTGTTCGTCAATTCCTCCGCATCCTCTTCTTTTCTTTGTATGTTCTCCAAAACCACCCTCTCTAAATCAGATAGTATGATTTTCACATTGACTGGTGAAGTCTGCCCAAACCGCCAGCAGCGACGTATCGCCTGGAAGTAACTTTCCCACGAGTCGCTAAGGCCAACAAACATCATATTGTGGCACCTCTGGAGGTTTAACCCGAACCCCGATATCCGAGTCTTGCTCAGCAGCACTCTTACTTTGCCCTCAGTGAAGCGAATGATGTTGTCCGTTTTGTAATCCAGCGTATCTTTACCCTCTATCAAAACCGCATCAGGTACCAGCTTGGCTAGTTGCCGTCCTTCCTCATTCAGCCCGCCCCACACAATCCACTGCTCATCTGAGTTGTTGAGTATATCCGCCGCAACTTCCACCTTCATCCTAACTGTATTCTTACGTGCCTCGCTTCTACCACGAATCCCAGATAGTTTAGTAGGAAATAGCTGCCCGCTAACTTGCGCTGATGCATCGCCTTTAGTCCAAACCGTCTCAACCGAGAGTGGCGGCAGGATATATCCATCGTCACTGAAGTTTATATCCGAAGGACGTTTCAACATTATTCCCCAGGATGCCAGCCATCTATAGAAGGCATTTCGCCCATGTCCTTTTAAGCGCCAGCCATCATCGTCGTGGATGAAGTACATGGAAAGCATTTCCTGTCGGCTCATGATTCCTAGGAATTCCGCATGGTTGGCAAGCTCGGCGATGTCATTCGGCGCTGGTGTAGCAGTGCAGCAGAGCTTATAAGGAGTATCCCTAAAAACTTCGATGAGCTTGGCTCTCGTCTTACCATCTACCGCCTTAAGTATGGAACTCTCATCTAGCACAACCGCACCAAATACTGATGAATCGAAGTGGTCTATTAACTCGTAGTTGGTGATGGCAATCCTAGTCTTAATCTGTGACTGGGAACGAGCATATCCAACTTCTACGCCGAGTTTCTCAGCCTCACGAATAGTTTGTTGTGCTACCGCTAATGGTGCAATGATAAGAGTCGGCACATCCAAAAGTCTTGCCCACTCCAATTGCTGGAAGGTCTTCCCCATACCTGTTGTTGTCCATATAGCACACCGCCCCTTCCTCAACGCCCATTTGACGATTACCTTCTGGAATGGGAAGAGCTTGCCGTTGATATCCTCTAGGGATACATCTATCCCCTTCGGCGGCACAGTCTGTAATTTGCTGGCTAGAAAGTCAGTGTAAGAATCCATTTGCCCCTCACTAGAAGAAATAAGCCTATGTAGAGTGTATTTCATACATAGGCTTAAGTCAATATTATTATGTCAACTTCCCTAACTAGATAGCTTCCACCACAAGCCACCACCACCACGGGCATTACGCCCATATGCAAGCAGTGGTACTGGATCGTTAACGTCCACCTGGAATGTCGCATAACCCTCTCTGGTGGCACCCTGGTACAGGTCGCCAGCTATTGAGGGTCTTGGGTCGAACACCACTAGCTGCTTCTCGTAGTCGCTACCGCTGGCACTCACTGCGGTAAAGTCCATCGTAGTGGTATGGTACTGCATATCCGGCTTTGCCTCTAACACCTTGAAGCGTAGCTCCACCACGATGTACTCCTTACCTGCCGCCGGTGGATCATTGAACTGGTTGGCCTCAGCCACCATCTGATTGGCATGTGCGCCTCTGTGTACTTCCAGCAGGGTGACAGCTACCTCGTAAGGCTCAGCGTTCTTGGTTACCTCCAGGGTAAGCTCTTCGCCTATACCTGCTGGATTACTGCGATTATGTCCTTTCACGTCCTCCACCTTTATCGCCGGTGCTACTGTAGATGTAGGTACTATCGTAGGTGCCACTGTAGGAATGGCCACTGGTGGAGCTGTAGTCAACGCTGAGGGGCTTGTCGGTGTCGGGGTGGCTACTACTATGGGTGGGGTAGCTGTAGGTACCTCTGTGGGCTTGGTGCCGCCACATCCTATTAGAAGTGCTGC'..b'CTCCTTTTGCGACCGAACAGGTCTGTTGCTCCATAACTTCATGGAGCGCAGATCTGTCTTCGGACTTTATCTTATCAAACTCGTCTATACAAACGAGGCCTTGATCGCCCAAAACTACAGCCCCCGCCTCGAGCATCATAATTCCGGATTTATCGCGAATTACTGCTGCTGTTAAACCTGCCGCAGTAGTACCTCTTCCTGAGGTATACAGACCTCTTGGTGCTATTTTTGCAGCAAATTTGAGCATTTCAGATTTGGCAGTACCTGGATCTCCAACGAGAAAGATATTGATATCTCCTCTACGATTTGAGCCATCAGCTAATTTCTTTGTTACCGATCCTACAATTAGTAAAAGAATAGATTCTTTAATTACTTCATGTCCATAAATATGAGGTGCAAATGATGCAATTAGTTTGTCATAATTATCTGGCATACTTGATAGAGCTAAGATCCGTTTTTCATCTTCTCTGCTTATAACTATTCTATCAACAGTTCTCTCATCTTTACTGTCAACAGTTCTCTCATCTTTATTCCCCAAAATTCCTCCAAGAAACTCTATATTGTTACCTTCCATGCGCAGTCTGAATAGACTTGTCCTTACTTGTAATGACTGCTCTTGCTCAATCCTGACTATCCCTGTCAACAAAACTCTATCTCCAGGTCTGCACCTGTCAACAAGATCATCCATAACAGTAACTTCTACATAATGCGGAAGTTGACCTGCGGGTAAATCTTCTGGTAGTTCTTGGATCCTAACTAGCTGGAAATCGGTAAAGTAGCTATGCTCTGGATCCATTTCAAGTTCCTTTTCAGAACACTGAGTACATCTCATAGGTTTCTTTAGGCTTAGACCTTTAAGCTGGGCTTCATTAAGAGTATTACAATTCAGACACGCGTATGCAATCTTTTTGGCAAGTGGTTTAATTTCAGAAGTCCTGACTACCATGCCAGGAACGCTTATCAACTTGTTTATCACATCTGCATTTATTTCTCTTAGCCCTTTTTGAACCGAATAATTTCCAATTCTTACTTTTATCTTGTCCTTAATTTCCTCAGCATAGTCGTAATGAATTTCTCTTAAGATTGAGTATACAGCTTTGTTAAAAGCGTCAAACATATCATCGGGTGTATCAGTAATTAATTTTGTTAGTTCTGGCTTATTTCTATCTAGGTCGATATAATCAACTACAATAAAGGTGGTATTTGATGCCATCATGTTATTAATTCTATCAAAATACTTGTAGTTTCCATCCCTGTCCTTATAGGCTCGTAAAAATGATTCTAATTCGTCTGATATTGCCGAAGTAGTTTGTTGCTTTTGCTCAGTCATTTACTTGTGCAACACCGATTCTTTAAAGGCCAATGAAGAAGTATGGACAAAATTATAAAGCTGTCTTTCCTCTGCAGATAATTTTGATTCTATTTCTGCGGAAAGTGACGAAGCAGCTGCTAGTTTCACAATTTTTCCAAGCCTGGACATCACGAATGAATTAAGTGATACCATTAGTGTTTCCCTTTCCTTTTCACTAAGACTTTCAAGAAAGTCATTTACACGAATGTAGAAGTCCGCTTCTATACCTGAAATATCATGTGGTTTTGCAATACGTTCTCTATTCAATGCCTTTGATACATAACTTGATATTTCATAATCTTGATTTTCAATTAAATTCTTATTCAACAAAATTTTTGTGAGCCATCTTGACAATGGTAAGATATCACCTTCCTTGGCATTGATGTGTATATCATTGAGAGATATTTTTACATCAGACTTGAATGTAACTCTAACTTCTTCAAGGAGATATTCAAGTAAGTATCTGTTTTTTAAGCTTTCAAATACGCTTTGAGTGAGAATGATGGATGACGACATATTGGGGATATAGTCTTAGAAATCTACTTAGTTAAACTTTACACGACCGATTAAATATCTGACAATTCGAACATCTTGTATGCCACAAACAGAGGCAAAAAACTTGTCAGATTTAATGTGGGTAGAAAAATACAGGCCTATTAAATTAGATGATGTTGTCAATCAAAAGGATATCGTAGAGAGTTTAAAGAACTTAATGAAAGAACCTGCTGGAATGCCGCACTTATTATTTACAGGTCCTGCTGGAGTTGGCAAAACTACTACTGCACTGTGTATGTCAAGACAATTACTTGGGGAAGATTGGAAGAGAGATACACTTGAGCTCAATGCCTCAGATGAAAGAGGAATAAAGATGGTTCGAGAAAGAGTTAAGGAATTTGCTTCCGTTTTCAAAATAAGAACAAGTGATAGGGAGGAAAGAAAATTTAGAATAATAATTTTAGATGAAGCCGATGAAATGACGTCCGAAGCCCAGACAGCTTTGCGAAGGATAATTGAAGATAGTTCTGAAACAACTCGTTTTGTTATAATATGTAATTATTTATCGCAGATTATTGAGCCTATTCAAAGTCGTTGTGCAATATTCAGATTTAAGAGAATTGAAAAAGAAATCATAGAGAATCATCTAAAATCATTATGTAAAAAAGAGGGAATTAAATATGATGATAAAGCAATTTCGCAAATTTTTGAATCCACAAATGGTGATCTGCGTCATTCAATAAACATTCTTCAAACTGCCGCTGTAATGGGATCGGTCAGTATTTTAAACGTCCAGGCATCCTTGGGACTTACTGGAAAATCAAAGGTAAGTGAAATAATCAAGCTGGCAATGTCAGGTAAATTTAATGAAGCCAGGGTCAAATTACTTGAATTAACTGCACTCTATGGAATGTCTGAATTCGATTTTCTAAAATATGCATACGAAGCCGTATACTCCTTAAAGTTATCCCACCCCGAAGACTTTGCTTCTCTAATAGCTGAATATGACTATCGTTTGACTCATGGGTCACATCCAGATATTCAGTTAACTGCGTTTTTAGCTCAATTGTCACGAATCGGTACCAAGCAGTAGAGTGGGGTTAGAAATAGTTACAGCTTGCGTTCAGATTATCGAATTATTAAATAAATTCTAATATGAAAAGCTGATTTATGCAATAGTCTTGTACTAAAAATTAATAATCTTCCTCAAATTCTTCTCCACCATCTTCTTCTTCGACTTCATCAAAGTCTTCTTCGAGCTCTTCTCTTTCTTCAGCGCTTTTATAAGGAAGATCGGCTTCACCGGCAGAATTGCAAACAGGACATTTGAATTCAATTGTCTGCCCTTCGAGGTCCAGAGGGAACTCTTTTGAGAAAACCTCATCGCATTTTGAACATACCAAAGTTGTCTGGATATTGTCAGTACTGAACTTGTGCGATTGTAGTCGAAATATGGTATTTGTCATTTCTTCCTACCTATTGAAATGGTCCTTTTTTATAAGGATTATTGTAATTTTTACTATACAGTATGTATTTTAGGTTTGGAATCATATATCAGAGCTAACAGATGTGCTCGGGCATCATTTTGGTCAACTAGACCACGATTTGCTATTGTTATTATTGTACTATTGTTTCTAACGCCTCGCATCTTCATACACAAATGCTCTCCTTCTGCAATCACAGTTACGCCTTTAACTCCCATTTTCATTATCTCGTCTGCGACTTCCTTTGTGAGTCTTTCTTGAATTTGCAATCTTTTAGAATATTTCTCTACCAGTCGTGCAAGTTTCGATATCCCAAAGACTTTGCCCGAAGGAGTGTAGGCAATGTGTATTCTGCCAAAAAAAGGAAGCATATGATGCTCACACATACTATAAAATTGAATGTCTTTAGCAATAATGGAATCAGTTTCTTCACTAAAACTAATTTCAAGCTCAGAATTCATGCAATACCCAGCAAAAATTTCTTCATACATATCTGCAATGCTTTTCGGAGTTCCCAGTAAACCCTCACGGTCCGGGTTTTCTCCGAGTTGCACTATCAGCTCCCTAACGAGTTTTTCTATCTTTCTTTTGTTAAATGAAGTTTTTTTCATGTTCTTTTTCCCCCTTTAATTATCTAGCACCTATTTCTTTATGTAGCTGTGGTATAA\n' |
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| diff -r 000000000000 -r eb22ba00cd4c test-data/phabox.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phabox.loc Tue Nov 12 09:32:16 2024 +0000 |
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| @@ -0,0 +1,1 @@ +phaboxdb phaboxdb 2 ${__HERE__}/phabox_db_v2/ \ No newline at end of file |
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| diff -r 000000000000 -r eb22ba00cd4c tool-data/phabox.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/phabox.loc.sample Tue Nov 12 09:32:16 2024 +0000 |
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| @@ -0,0 +1,2 @@ +# Format: +# value name version path \ No newline at end of file |
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| diff -r 000000000000 -r eb22ba00cd4c tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Nov 12 09:32:16 2024 +0000 |
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| @@ -0,0 +1,7 @@ +<tables> + <!-- phabox reference data --> + <table name="phabox" comment_char="#"> + <columns>value, name, version, path</columns> + <file path="tool-data/phabox.loc" /> + </table> +</tables> |
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| diff -r 000000000000 -r eb22ba00cd4c tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Tue Nov 12 09:32:16 2024 +0000 |
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| @@ -0,0 +1,6 @@ +<tables> + <table name="phabox" comment_char="#"> + <columns>value, name, version, path</columns> + <file path="${__HERE__}/test-data/phabox.loc" /> + </table> +</tables> |