bgruening · SaimMomin12 · May 14, 2025 · Apr 3, 2025 · Apr 3, 2025 · Apr 24, 2025
diff --git a/tools/vrhyme/.shed.yml b/tools/vrhyme/.shed.yml
@@ -0,0 +1,9 @@
+name: vrhyme
+owner: bgruening
+description: Tool for dereplication and binning virus genomes from metagenomes.
+homepage_url: https://github.com/AnantharamanLab/vRhyme
+long_description:
+    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.
+remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/vrhyme
+categories:
+  - Metagenomics
diff --git a/tools/vrhyme/macros.xml b/tools/vrhyme/macros.xml
@@ -0,0 +1,23 @@
+<macros>
+    <token name="@TOOL_VERSION@">1.1.0</token>
+    <token name="@VERSION_SUFFIX@">galaxy0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">vrhyme</requirement>
+            <requirement type="package" version="3.23">mummer</requirement>
+            <requirement type="package" version="1.1.3">scikit-learn</requirement>
+            <requirement type="package" version="2.2.1">bwa-mem2</requirement>
+            <requirement type="package" version="2.5.4">bowtie2</requirement>
+        </requirements>
+    </xml>
+    <xml name="biotools">
+        <xrefs>
+            <xref type="bio.tools">vRhyme</xref>
+        </xrefs>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/nar/gkac341</citation>
+        </citations>
+    </xml>
+</macros>
diff --git a/tools/vrhyme/test-data/Test_simulated.bam b/tools/vrhyme/test-data/Test_simulated.bam
diff --git a/tools/vrhyme/test-data/Test_simulated.fastq b/tools/vrhyme/test-data/Test_simulated.fastq
diff --git a/tools/vrhyme/test-data/Test_simulated_1.fastq b/tools/vrhyme/test-data/Test_simulated_1.fastq
diff --git a/tools/vrhyme/test-data/Test_simulated_2.fastq b/tools/vrhyme/test-data/Test_simulated_2.fastq
diff --git a/tools/vrhyme/test-data/example_coverage_values.tsv b/tools/vrhyme/test-data/example_coverage_values.tsv
@@ -0,0 +1,13 @@
+scaffold	avg_SRR2046222_trim	stdev_SRR2046222_trim	avg_SRR2046235_trim	stdev_SRR2046235_trim	avg_SRR2046236_trim	stdev_SRR2046236_trim
+virus_1__0:13792	96.32359338747099	24.813803138227193	336.82207076566124	48.53375006850304	292.5810614849188	50.93065819442028
+virus_1__13792:29888	87.37972166998011	21.574192260474437	342.9219681908549	45.861610044217755	289.34505467196817	48.29033273320929
+virus_1__29888:34019	91.07334785766159	23.463248535880197	355.4468651658194	65.05538501584905	294.38828370854515	61.928534242372756
+virus_1__34019:45164	91.42009869896815	25.906158249588273	348.6326603858232	49.327479050402346	287.1410497981158	49.03400296998417
+virus_1__45164:63646	88.59002375296912	23.092473303597128	323.18004750593826	77.47367574377701	265.3235154394299	56.6744031670385
+virus_2__0:13100	101.29984732824427	27.351034700963805	441.32977099236643	62.53809305658163	297.72587786259544	49.31367633676957
+virus_2__13100:24602	103.90975482524779	28.36762220733677	450.5150408624587	63.64019699678692	297.76864893062077	59.07434359506686
+virus_2__24602:37063	103.00722253430703	26.666693441816133	442.6597383837573	62.15227015869699	290.2397881389937	50.04145100932727
+virus_2__37063:44358	104.55274955170353	28.469833814916036	442.5375074716079	68.57615997501904	309.4928272564256	53.75696434636587
+virus_3__0:6773	8497.161466885605	1752.9154817117605	14112.200328407225	2891.864467713525	30100.58401751505	6225.80141987776
+virus_4__0:8428	0.23421926910299004	1.1266316629605762	19.504983388704318	9.602139891487262	22.572259136212626	11.527000319991355
+virus_5__0:8378	0.4128929142248269	1.0539541679344029	118.62892914224827	25.736327963856304	36.50879062333511	16.065928782271936
diff --git a/tools/vrhyme/test-data/example_scaffolds.fasta b/tools/vrhyme/test-data/example_scaffolds.fasta
diff --git a/tools/vrhyme/test-data/example_scaffolds.prodigal.faa b/tools/vrhyme/test-data/example_scaffolds.prodigal.faa
diff --git a/tools/vrhyme/test-data/example_scaffolds.prodigal.ffn b/tools/vrhyme/test-data/example_scaffolds.prodigal.ffn
diff --git a/tools/vrhyme/test-data/example_scaffolds_replication.fasta b/tools/vrhyme/test-data/example_scaffolds_replication.fasta
diff --git a/tools/vrhyme/test-data/output_coverage-table/vRhyme_best_bins_fasta/vRhyme_bin_1.faa b/tools/vrhyme/test-data/output_coverage-table/vRhyme_best_bins_fasta/vRhyme_bin_1.faa
diff --git a/tools/vrhyme/test-data/output_coverage-table/vRhyme_best_bins_fasta/vRhyme_bin_1.fasta b/tools/vrhyme/test-data/output_coverage-table/vRhyme_best_bins_fasta/vRhyme_bin_1.fasta
diff --git a/tools/vrhyme/test-data/output_coverage-table/vRhyme_best_bins_fasta/vRhyme_bin_1.ffn b/tools/vrhyme/test-data/output_coverage-table/vRhyme_best_bins_fasta/vRhyme_bin_1.ffn
diff --git a/tools/vrhyme/vrhyme.xml b/tools/vrhyme/vrhyme.xml