usegalaxy-au · galaxy-au-tools-jenkins-bot · Aug 7, 2024
diff --git a/_posts/2024-08-07-tool-updates.md b/_posts/2024-08-07-tool-updates.md
@@ -0,0 +1,63 @@
+---
+site: freiburg
+title: 'Galaxy Australia tool updates 2024-08-07'
+tags: [tools]
+supporters:
+    - galaxyaustralia
+    - melbinfo
+    - qcif
+---
+
+
+<style>
+  table {
+    width: 100%;
+    margin: 10px 20px;
+  }
+  table th {
+    display: none;
+  }
+  td {
+    padding: 3px 5px;
+  }
+  tr td:nth-child(1) {
+    vertical-align: top;
+    width: 25%;
+  }
+</style>
+
+### Tools installed
+
+| Section | Tool |
+|---------|-----|
+| **Annotation** | find_subsequences [d882a0a75759](https://toolshed.g2.bx.psu.edu/view/bgruening/find_subsequences/d882a0a75759)<br/>plasmidfinder [7075b7a5441b](https://toolshed.g2.bx.psu.edu/view/iuc/plasmidfinder/7075b7a5441b) |
+| **Assembly** | megahit_contig2fastg [4ec5b3777508](https://toolshed.g2.bx.psu.edu/view/iuc/megahit_contig2fastg/4ec5b3777508) |
+| **ChemicalToolBox** | align_it [06d9381593a4](https://toolshed.g2.bx.psu.edu/view/bgruening/align_it/06d9381593a4)<br/>ctb_im_rxn_maker [8ef5428fb809](https://toolshed.g2.bx.psu.edu/view/bgruening/ctb_im_rxn_maker/8ef5428fb809)<br/>mdanalysis_distance [fd987ff06ceb](https://toolshed.g2.bx.psu.edu/view/chemteam/mdanalysis_distance/fd987ff06ceb)<br/>mdanalysis_ramachandran_plot [be5eaea0b2d1](https://toolshed.g2.bx.psu.edu/view/chemteam/mdanalysis_ramachandran_plot/be5eaea0b2d1)<br/>mdanalysis_rdf [49076afc90b1](https://toolshed.g2.bx.psu.edu/view/chemteam/mdanalysis_rdf/49076afc90b1)<br/>openbabel_addh [6e4b7e0c61a6](https://toolshed.g2.bx.psu.edu/view/bgruening/openbabel_addh/6e4b7e0c61a6)<br/>openbabel_remduplicates [b2569e22b40c](https://toolshed.g2.bx.psu.edu/view/bgruening/openbabel_remduplicates/b2569e22b40c)<br/>qed [52a8d34dd08f](https://toolshed.g2.bx.psu.edu/view/bgruening/qed/52a8d34dd08f)<br/>rdconf [5c501eb8d56c](https://toolshed.g2.bx.psu.edu/view/bgruening/rdconf/5c501eb8d56c) |
+| **Collection Operations** | split_file_on_column [ff2a81aa3f08](https://toolshed.g2.bx.psu.edu/view/bgruening/split_file_on_column/ff2a81aa3f08) |
+| **Get Data** | ega_download_client [7d87a9d58aa1](https://toolshed.g2.bx.psu.edu/view/iuc/ega_download_client/7d87a9d58aa1) |
+| **HiCExplorer** | hicexplorer_hicplottads [50171f863420](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplottads/50171f863420) |
+| **Imaging** | 2d_split_binaryimage_by_watershed [f8f7987586b7](https://toolshed.g2.bx.psu.edu/view/imgteam/2d_split_binaryimage_by_watershed/f8f7987586b7)<br/>idr_download_by_ids [4b794652dcdc](https://toolshed.g2.bx.psu.edu/view/iuc/idr_download_by_ids/4b794652dcdc)<br/>overlay_images [8dc02c854048](https://toolshed.g2.bx.psu.edu/view/imgteam/overlay_images/8dc02c854048) |
+| **Metagenomic Analysis** | polypolish [f355085dd2aa](https://toolshed.g2.bx.psu.edu/view/iuc/polypolish/f355085dd2aa)<br/>recentrifuge [d4fbfd31696c](https://toolshed.g2.bx.psu.edu/view/iuc/recentrifuge/d4fbfd31696c)<br/>phyloseq_from_dada2 [87064cb77a52](https://toolshed.g2.bx.psu.edu/view/iuc/phyloseq_from_dada2/87064cb77a52) |
+| **Phylogenetics** | rapidnj [9f4a66e22580](https://toolshed.g2.bx.psu.edu/view/iuc/rapidnj/9f4a66e22580) |
+| **RNA-seq** | chira_collapse [05996586c8b3](https://toolshed.g2.bx.psu.edu/view/iuc/chira_collapse/05996586c8b3)<br/>chira_extract [73d2b7a8d94b](https://toolshed.g2.bx.psu.edu/view/iuc/chira_extract/73d2b7a8d94b)<br/>chira_map [7925dd016f53](https://toolshed.g2.bx.psu.edu/view/iuc/chira_map/7925dd016f53)<br/>chira_merge [9930af9d17f8](https://toolshed.g2.bx.psu.edu/view/iuc/chira_merge/9930af9d17f8)<br/>chira_quantify [38d2b1f38992](https://toolshed.g2.bx.psu.edu/view/iuc/chira_quantify/38d2b1f38992) |
+| **SAM/BAM** | bamtools [970e6333f07e](https://toolshed.g2.bx.psu.edu/view/devteam/bamtools/970e6333f07e) |
+| **Single-cell** | droplet_barcode_plot [8f605643ccfd](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/droplet_barcode_plot/8f605643ccfd)<br/>dropletutils_empty_drops [fa662ca7ae7f](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/dropletutils_empty_drops/fa662ca7ae7f)<br/>dropletutils_read_10x [ca62f52e0d7f](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/dropletutils_read_10x/ca62f52e0d7f)<br/>run_sccaf [647d34f125bc](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/run_sccaf/647d34f125bc)<br/>sccaf_asses [37a4c22f600b](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/sccaf_asses/37a4c22f600b)<br/>sccaf_regress_out [5ef0610e9f50](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/sccaf_regress_out/5ef0610e9f50)<br/>seurat_create_seurat_object [f8865ae30723](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/seurat_create_seurat_object/f8865ae30723)<br/>seurat_dim_plot [64174ac50d78](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/seurat_dim_plot/64174ac50d78)<br/>seurat_export_cellbrowser [36221da750e8](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/seurat_export_cellbrowser/36221da750e8)<br/>seurat_filter_cells [cd9f564bd63f](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/seurat_filter_cells/cd9f564bd63f)<br/>seurat_find_clusters [d541e9e62beb](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/seurat_find_clusters/d541e9e62beb)<br/>seurat_find_markers [07fc9f4841b3](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/seurat_find_markers/07fc9f4841b3)<br/>seurat_find_neighbours [ba897c57bdd9](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/seurat_find_neighbours/ba897c57bdd9)<br/>seurat_find_variable_genes [948fc0276b4f](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/seurat_find_variable_genes/948fc0276b4f)<br/>seurat_normalise_data [3f49bc9c9213](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/seurat_normalise_data/3f49bc9c9213)<br/>seurat_plot [95d79f1134f0](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/seurat_plot/95d79f1134f0)<br/>seurat_read10x [f5db0e853f57](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/seurat_read10x/f5db0e853f57)<br/>seurat_run_pca [8ded486b0014](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/seurat_run_pca/8ded486b0014)<br/>seurat_run_tsne [0db997e4a81d](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/seurat_run_tsne/0db997e4a81d)<br/>seurat_run_umap [b9424c715a0d](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/seurat_run_umap/b9424c715a0d)<br/>seurat_scale_data [5e9ba303f9e1](https://toolshed.g2.bx.psu.edu/view/ebi-gxa/seurat_scale_data/5e9ba303f9e1) |
+| **Text Manipulation** | add_input_name_as_column [3284b72eef56](https://toolshed.g2.bx.psu.edu/view/mvdbeek/add_input_name_as_column/3284b72eef56) |
+| **Variant Calling** | control_freec [f923c54a17ee](https://toolshed.g2.bx.psu.edu/view/iuc/control_freec/f923c54a17ee) |
+
+### Tools updated
+
+| Section | Tool |
+|---------|-----|
+| **Annotation** | cpat [7ccc6234b54e](https://toolshed.g2.bx.psu.edu/view/bgruening/cpat/7ccc6234b54e)<br/>funannotate_clean [8e1ace8f77c6](https://toolshed.g2.bx.psu.edu/view/iuc/funannotate_clean/8e1ace8f77c6)<br/>funannotate_sort [d77fdcca400e](https://toolshed.g2.bx.psu.edu/view/iuc/funannotate_sort/d77fdcca400e) |
+| **Assembly** | genomescope [460fad600dce](https://toolshed.g2.bx.psu.edu/view/iuc/genomescope/460fad600dce)<br/>salsa [58a870ef434c](https://toolshed.g2.bx.psu.edu/view/iuc/salsa/58a870ef434c) |
+| **BED** | bedtools [64e2edfe7a2c](https://toolshed.g2.bx.psu.edu/view/iuc/bedtools/64e2edfe7a2c) |
+| **Bacterial Typing** | integron_finder [bfd290fe1588](https://toolshed.g2.bx.psu.edu/view/iuc/integron_finder/bfd290fe1588) |
+| **FASTA/FASTQ** | cutadapt [5eb7e84243f2](https://toolshed.g2.bx.psu.edu/view/lparsons/cutadapt/5eb7e84243f2) |
+| **FASTQ Quality Control** | fastqc [2c64fded1286](https://toolshed.g2.bx.psu.edu/view/devteam/fastqc/2c64fded1286) |
+| **Get Data** | uniprot_rest_interface [468c71dac78a](https://toolshed.g2.bx.psu.edu/view/bgruening/uniprot_rest_interface/468c71dac78a) |
+| **Mapping** | minimap2 [5cc34c3f440d](https://toolshed.g2.bx.psu.edu/view/iuc/minimap2/5cc34c3f440d) |
+| **Metagenomic Analysis** | bracken [0c7b6eb7e752](https://toolshed.g2.bx.psu.edu/view/iuc/bracken/0c7b6eb7e752)<br/>dada2_assigntaxonomyaddspecies [65db807336bc](https://toolshed.g2.bx.psu.edu/view/iuc/dada2_assigntaxonomyaddspecies/65db807336bc)<br/>kraken2 [cdee7158adf3](https://toolshed.g2.bx.psu.edu/view/iuc/kraken2/cdee7158adf3)<br/>krakentools_combine_kreports [4960abe31b4d](https://toolshed.g2.bx.psu.edu/view/iuc/krakentools_combine_kreports/4960abe31b4d) |
+| **Nanopore** | dorado_pod5_convert [7c47b3c9e493](https://toolshed.g2.bx.psu.edu/view/galaxy-australia/dorado_pod5_convert/7c47b3c9e493) |
+| **Single-cell** | alevin [e32b215b7c04](https://toolshed.g2.bx.psu.edu/view/bgruening/alevin/e32b215b7c04), [e4c01dcece8b](https://toolshed.g2.bx.psu.edu/view/bgruening/alevin/e4c01dcece8b), [f2000bc73102](https://toolshed.g2.bx.psu.edu/view/bgruening/alevin/f2000bc73102)<br/>dropletutils [cfe1e6c28d95](https://toolshed.g2.bx.psu.edu/view/iuc/dropletutils/cfe1e6c28d95)<br/>modify_loom [59be31ac9dc3](https://toolshed.g2.bx.psu.edu/view/iuc/modify_loom/59be31ac9dc3), [7784821452ac](https://toolshed.g2.bx.psu.edu/view/iuc/modify_loom/7784821452ac), [eeab712b0b99](https://toolshed.g2.bx.psu.edu/view/iuc/modify_loom/eeab712b0b99)<br/>raceid_clustering [a4b734cd253b](https://toolshed.g2.bx.psu.edu/view/iuc/raceid_clustering/a4b734cd253b), [c4f39bf4a068](https://toolshed.g2.bx.psu.edu/view/iuc/raceid_clustering/c4f39bf4a068)<br/>raceid_filtnormconf [43c146e25a43](https://toolshed.g2.bx.psu.edu/view/iuc/raceid_filtnormconf/43c146e25a43), [d45f092caf24](https://toolshed.g2.bx.psu.edu/view/iuc/raceid_filtnormconf/d45f092caf24)<br/>raceid_trajectory [72979cac22b2](https://toolshed.g2.bx.psu.edu/view/iuc/raceid_trajectory/72979cac22b2), [e93b008c637a](https://toolshed.g2.bx.psu.edu/view/iuc/raceid_trajectory/e93b008c637a)<br/>scanpy_normalize [f3ad813a58a3](https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_normalize/f3ad813a58a3)<br/>scanpy_remove_confounders [e66884b1c1a5](https://toolshed.g2.bx.psu.edu/view/iuc/scanpy_remove_confounders/e66884b1c1a5) |
+| **iVar** | ivar_trim [a250929be21b](https://toolshed.g2.bx.psu.edu/view/iuc/ivar_trim/a250929be21b) |