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MinamehrSaimMomin12
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SaimMomin12
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Add vrhyme tool (#1600)
* add vrhyme tool * update the xml file and the test-data * Updated the xml file and test-data * Updated the xml file * Updated the xml file * Updated the xml file and test-data * Updated the xml file and test-data * Updated the xml file and test-data * test-data * Updated the xml file * Updated the xml file and test-data * Update Profile Version * Remove empty line * Remove empty line * Include additional format * Capitalize * Refactor title * Refactor title * Refactor title * Add more file format * Adding missing dependencies * Capitalize * Update tools/vrhyme/vrhyme.xml * Update tools/vrhyme/vrhyme.xml --------- Co-authored-by: Saim Momin <64724322+SaimMomin12@users.noreply.github.com>
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‎tools/vrhyme/.shed.yml‎

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name: vrhyme
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owner: bgruening
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description: Tool for dereplication and binning virus genomes from metagenomes.
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homepage_url: https://github.com/AnantharamanLab/vRhyme
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long_description:
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vRhyme is a tool for binning viral genomes from metagenomes. It groups viral contigs into metagenome-assembled genomes (vMAGs) using sequence features, read coverage patterns, and machine learning. It also includes an optional dereplication function to remove redundant sequences.
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remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/vrhyme
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categories:
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- Metagenomics

‎tools/vrhyme/macros.xml‎

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<macros>
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<token name="@TOOL_VERSION@">1.1.0</token>
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<token name="@VERSION_SUFFIX@">galaxy0</token>
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<xml name="requirements">
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<requirements>
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<requirement type="package" version="@TOOL_VERSION@">vrhyme</requirement>
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<requirement type="package" version="3.23">mummer</requirement>
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<requirement type="package" version="1.1.3">scikit-learn</requirement>
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<requirement type="package" version="2.2.1">bwa-mem2</requirement>
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<requirement type="package" version="2.5.4">bowtie2</requirement>
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</requirements>
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</xml>
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<xml name="biotools">
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<xrefs>
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<xref type="bio.tools">vRhyme</xref>
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</xrefs>
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</xml>
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<xml name="citations">
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<citations>
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<citation type="doi">10.1093/nar/gkac341</citation>
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</citations>
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</xml>
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</macros>

‎tools/vrhyme/test-data/Test_simulated.bam‎

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‎tools/vrhyme/test-data/Test_simulated.fastq‎

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‎tools/vrhyme/test-data/Test_simulated_1.fastq‎

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‎tools/vrhyme/test-data/Test_simulated_2.fastq‎

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‎tools/vrhyme/test-data/example_coverage_values.tsv‎

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scaffold avg_SRR2046222_trim stdev_SRR2046222_trim avg_SRR2046235_trim stdev_SRR2046235_trim avg_SRR2046236_trim stdev_SRR2046236_trim
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virus_1__0:13792 96.32359338747099 24.813803138227193 336.82207076566124 48.53375006850304 292.5810614849188 50.93065819442028
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virus_1__13792:29888 87.37972166998011 21.574192260474437 342.9219681908549 45.861610044217755 289.34505467196817 48.29033273320929
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virus_1__29888:34019 91.07334785766159 23.463248535880197 355.4468651658194 65.05538501584905 294.38828370854515 61.928534242372756
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virus_1__34019:45164 91.42009869896815 25.906158249588273 348.6326603858232 49.327479050402346 287.1410497981158 49.03400296998417
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virus_1__45164:63646 88.59002375296912 23.092473303597128 323.18004750593826 77.47367574377701 265.3235154394299 56.6744031670385
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virus_2__0:13100 101.29984732824427 27.351034700963805 441.32977099236643 62.53809305658163 297.72587786259544 49.31367633676957
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virus_2__13100:24602 103.90975482524779 28.36762220733677 450.5150408624587 63.64019699678692 297.76864893062077 59.07434359506686
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virus_2__24602:37063 103.00722253430703 26.666693441816133 442.6597383837573 62.15227015869699 290.2397881389937 50.04145100932727
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virus_2__37063:44358 104.55274955170353 28.469833814916036 442.5375074716079 68.57615997501904 309.4928272564256 53.75696434636587
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virus_3__0:6773 8497.161466885605 1752.9154817117605 14112.200328407225 2891.864467713525 30100.58401751505 6225.80141987776
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virus_4__0:8428 0.23421926910299004 1.1266316629605762 19.504983388704318 9.602139891487262 22.572259136212626 11.527000319991355
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virus_5__0:8378 0.4128929142248269 1.0539541679344029 118.62892914224827 25.736327963856304 36.50879062333511 16.065928782271936

‎tools/vrhyme/test-data/example_scaffolds.fasta‎

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‎tools/vrhyme/test-data/example_scaffolds.prodigal.faa‎

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‎tools/vrhyme/test-data/example_scaffolds.prodigal.ffn‎

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