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fetch all tools bot - step filter
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github-actions committed Mar 31, 2024
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2 changes: 1 addition & 1 deletion results/imaging/index.html
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<td>bgruening</td>
<td>https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/</td>
<td>https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick</td>
<td>1.3.42</td>
<td>1.3.43</td>
<td>graphicsmagick</td>
<td>1.3.26</td>
<td>(1/3)</td>
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2 changes: 1 addition & 1 deletion results/imaging/tools.tsv
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Expand Up @@ -49,7 +49,7 @@ cellpose cellpose Cellpose is an anatomical segmentation algorithm To u
cellprofiler cp_cellprofiler, cp_color_to_gray, cp_convert_objects_to_image, cp_display_data_on_image, cp_enhance_or_suppress_features, cp_export_to_spreadsheet, cp_gray_to_color, cp_identify_primary_objects, cp_image_math, cp_mask_image, cp_measure_granularity, cp_measure_image_area_occupied, cp_measure_image_intensity, cp_measure_image_quality, cp_measure_object_intensity, cp_measure_object_size_shape, cp_measure_texture, cp_overlay_outlines, cp_relate_objects, cp_save_images, cp_common, cp_tile, cp_track_objects cellProfiler wrapper CellProfiler CellProfiler cellprofiler CellProfiler Tool for quantifying data from biological images, particularly in high-throughput experiments. Quantification, Image analysis, Parsing Imaging, Microarray experiment, Genotype and phenotype To update Imaging cellprofiler bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler (0/23) (23/23) (23/23) (19/23) False
cellprofiler_v4 cp_cellprofiler4 cellProfiler4 wrapper To update Imaging cellprofiler4 bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/cellprofiler_v4 4.2.6 (0/1) (0/1) (1/1) (1/1) False
bia-ftplinks bia_download Tool to query ftp links for study from bioimage archive To update Imaging bia_download bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/bia-ftplinks 0.1.0 wget (0/1) (0/1) (1/1) (0/1) False
graphicsmagick graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage Contains tools based on GraphicsMagick To update http://www.graphicsmagick.org Imaging graphicsmagick bgruening https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/ https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick 1.3.42 graphicsmagick 1.3.26 (1/3) (0/3) (3/3) (0/3) False
graphicsmagick graphicsmagick_image_compare, graphicsmagick_image_convert, graphicsmagick_image_montage Contains tools based on GraphicsMagick To update http://www.graphicsmagick.org Imaging graphicsmagick bgruening https://github.com/bgruening/galaxytools/new/gm/tools/image_processing/image_processing/ https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/graphicsmagick 1.3.43 graphicsmagick 1.3.26 (1/3) (0/3) (3/3) (0/3) False
imagej2 imagej2_adjust_threshold_binary, imagej2_analyze_particles_binary, imagej2_analyze_skeleton, imagej2_binary_to_edm, imagej2_bunwarpj_adapt_transform, imagej2_bunwarpj_align, imagej2_bunwarpj_compare_elastic, imagej2_bunwarpj_compare_elastic_raw, imagej2_bunwarpj_compare_raw, imagej2_bunwarpj_compose_elastic, imagej2_bunwarpj_compose_raw, imagej2_bunwarpj_compose_raw_elastic, imagej2_bunwarpj_convert_to_raw, imagej2_bunwarpj_elastic_transform, imagej2_bunwarpj_raw_transform, imagej2_create_image, imagej2_enhance_contrast, imagej2_find_edges, imagej2_find_maxima, imagej2_make_binary, imagej2_math, imagej2_noise, imagej2_shadows, imagej2_sharpen, imagej2_skeletonize3d, imagej2_smooth, imagej2_watershed_binary ImageJ2 is a new version of ImageJ for the next generation of multidimensionalimage data, with a focus on scientific imaging. imagej imagej imagej2 ImageJ2 It is a public domain Java image processing program, which was designed with an open architecture. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems. Image analysis, Image annotation, Visualisation Imaging To update http://fiji.sc Imaging imagej2 imgteam https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 (0/27) (0/27) (27/27) (0/27) False
woundhealing woundhealing_scratch_assay Tool to automate quantification of wound healing in high-throughput microscopy scratch assays Up-to-date https://git.embl.de/grp-cba/wound-healing-htm-screen Imaging Wound healing scratch assay image analysis bgruening https://github.com/bgruening/galaxytools/tree/master/tools https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/woundhealing 1.6.1 fiji-morpholibj 1.6.1 (0/1) (0/1) (1/1) (0/1) False
spyboat 67.0 1.0 spyboat Wavelet analysis for 3d-image stacks To update http://github.com/tensionhead/spyboat Imaging, Graphics spyboat iuc https://github.com/galaxyproject/tools-iuc/tree/master/packages/spyboat https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat 0.1.2 spyboat (0/1) (0/1) (1/1) (0/1) False
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108 changes: 83 additions & 25 deletions results/microgalaxy/index.html
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<td>1.0.17</td>
<td>(0/1)</td>
<td>(0/1)</td>
<td>(0/1)</td>
<td>(1/1)</td>
<td>(0/1)</td>
</tr>
<tr>
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<td>(3/3)</td>
<td>(0/3)</td>
</tr>
<tr>
<td></td>
<td>colabfold</td>
<td></td>
<td></td>
<td>colabfold_alphafold, colabfold_msa</td>
<td>Protein prediction based on AlphaFold2</td>
<td>Colabfold</td>
<td>Colabfold</td>
<td></td>
<td>ColabFold</td>
<td>ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures.</td>
<td>Database search, Protein structure prediction, Fold recognition</td>
<td>Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics</td>
<td>To update</td>
<td>https://github.com/sokrypton/ColabFold</td>
<td>Proteomics, Graphics</td>
<td>colabfold</td>
<td>iuc</td>
<td>https://github.com/sokrypton/ColabFold</td>
<td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold</td>
<td>1.5.5</td>
<td></td>
<td></td>
<td>(0/2)</td>
<td>(0/2)</td>
<td>(0/2)</td>
<td>(0/2)</td>
</tr>
<tr>
<td></td>
<td>compleasm</td>
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<td>"Compleasm: a faster and more accurate reimplementation of BUSCO"</td>
<td>Sequence assembly validation, Sequence analysis, Scaffolding, Transcriptome assembly</td>
<td>Sequence assembly, Genomics, Transcriptomics, Sequence analysis</td>
<td>To update</td>
<td>Up-to-date</td>
<td>https://github.com/huangnengCSU/compleasm</td>
<td>Sequence Analysis</td>
<td>compleasm</td>
<td>iuc</td>
<td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/</td>
<td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm</td>
<td>0.2.5</td>
<td>0.2.6</td>
<td>compleasm</td>
<td>0.2.6</td>
<td>(0/1)</td>
Expand All @@ -3986,7 +4015,7 @@
<td>A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.</td>
<td>Sequence clustering, Read binning</td>
<td>Metagenomics</td>
<td>Up-to-date</td>
<td>To update</td>
<td>https://github.com/BinPro/CONCOCT</td>
<td>Metagenomics</td>
<td>concoct</td>
Expand All @@ -3995,7 +4024,7 @@
<td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct</td>
<td>1.1.0</td>
<td>concoct</td>
<td>1.1.0</td>
<td></td>
<td>(0/5)</td>
<td>(0/5)</td>
<td>(5/5)</td>
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<td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram</td>
<td>1.3.5</td>
<td>dram</td>
<td>1.4.6</td>
<td>1.5.0</td>
<td>(0/5)</td>
<td>(0/5)</td>
<td>(5/5)</td>
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<td>Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species.</td>
<td>Sequence alignment, Protein sequence analysis</td>
<td>Sequence sites, features and motifs, Sequence analysis</td>
<td>To update</td>
<td>Up-to-date</td>
<td>https://github.com/lh3/miniprot</td>
<td>Sequence Analysis</td>
<td></td>
<td>iuc</td>
<td>https://github.com/galaxyproject/tools-iuc/tree/master/tools/miniprot</td>
<td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot</td>
<td>0.12</td>
<td>0.13</td>
<td>miniprot</td>
<td>0.13</td>
<td>(0/2)</td>
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<td>(1/1)</td>
<td>(1/1)</td>
</tr>
<tr>
<td></td>
<td>pairtools</td>
<td></td>
<td></td>
<td>pairtools_parse</td>
<td>Flexible tools for Hi-C data processing</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td>Up-to-date</td>
<td>https://pairtools.readthedocs.io</td>
<td>Sequence Analysis</td>
<td>pairtools</td>
<td>iuc</td>
<td>https://github.com/open2c/pairtools</td>
<td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools</td>
<td>1.0.3</td>
<td>pairtools</td>
<td>1.0.3</td>
<td>(0/1)</td>
<td>(0/1)</td>
<td>(0/1)</td>
<td>(0/1)</td>
</tr>
<tr>
<td></td>
<td>pharokka</td>
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<td>1.46.0</td>
<td>(0/4)</td>
<td>(0/4)</td>
<td>(3/4)</td>
<td>(4/4)</td>
<td>(0/4)</td>
</tr>
<tr>
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<td>0.1.6</td>
<td>(0/2)</td>
<td>(0/2)</td>
<td>(0/2)</td>
<td>(2/2)</td>
<td>(0/2)</td>
</tr>
<tr>
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<td>seqkit</td>
<td></td>
<td></td>
<td>seqkit_fx2tab, seqkit_locate, seqkit_stats</td>
<td>seqkit_fx2tab, seqkit_locate, seqkit_sort, seqkit_stats, seqkit_translate</td>
<td>A cross-platform and ultrafast toolkit for FASTA/Q file manipulation</td>
<td>seqkit</td>
<td>seqkit</td>
Expand All @@ -7679,10 +7737,10 @@
<td>2.3.1</td>
<td>seqkit</td>
<td>2.8.0</td>
<td>(0/3)</td>
<td>(0/3)</td>
<td>(3/3)</td>
<td>(2/3)</td>
<td>(0/5)</td>
<td>(2/5)</td>
<td>(3/5)</td>
<td>(2/5)</td>
</tr>
<tr>
<td></td>
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<td>spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades</td>
<td>SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction.</td>
<td>spades</td>
<td>rnaspades, spades, plasmidspades, metaviralspades, coronaspades, metaspades, metaplasmidspades, biosyntheticspades, rnaviralspades</td>
<td>plasmidspades, rnaspades, spades, coronaspades, metaspades, metaviralspades, biosyntheticspades, metaplasmidspades, rnaviralspades</td>
<td></td>
<td>SPAdes</td>
<td>St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads.</td>
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<td>https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler</td>
<td>4.4.1</td>
<td>tb-profiler</td>
<td>6.1.0</td>
<td>6.2.0</td>
<td>(1/1)</td>
<td>(1/1)</td>
<td>(1/1)</td>
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<td>1.70</td>
<td>(0/3)</td>
<td>(0/3)</td>
<td>(0/3)</td>
<td>(3/3)</td>
<td>(3/3)</td>
</tr>
<tr>
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<td>190.0</td>
<td>msconvert</td>
<td>msconvert Convert and/or filter mass spectrometry files (including vendor formats) using the official Docker container</td>
<td>msconvert</td>
<td>msconvert</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
<td>msConvert</td>
<td>msConvert is a command-line utility for converting between various mass spectrometry data formats, including from raw data from several commercial companies (with vendor libraries, Windows-only). For Windows users, there is also a GUI, msConvertGUI.</td>
<td>Filtering, Formatting</td>
<td>Proteomics, Proteomics experiment</td>
<td>To update</td>
<td></td>
<td>http://proteowizard.sourceforge.net/tools.shtml</td>
<td>Proteomics</td>
<td>msconvert</td>
<td>galaxyp</td>
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