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<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="4.0.0">Jekyll</generator><link href="https://galaxyproject.eu/feed.xml" rel="self" type="application/atom+xml" /><link href="https://galaxyproject.eu/" rel="alternate" type="text/html" /><updated>2023-12-11T02:52:35+01:00</updated><id>https://galaxyproject.eu/feed.xml</id><title type="html">Galaxy Europe</title><subtitle>The European Galaxy Instance</subtitle><entry><title type="html">UseGalaxy.eu Tool Updates for 2023-12-10</title><link href="https://galaxyproject.eu/posts/2023/12/10/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2023-12-10" /><published>2023-12-10T00:00:00+01:00</published><updated>2023-12-10T00:00:00+01:00</updated><id>https://galaxyproject.eu/posts/2023/12/10/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2023/12/10/tool-update/">&lt;p&gt;On 2023-12-10, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in &lt;a href=&quot;https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#422/&quot;&gt;Jenkins Build #422&lt;/a&gt;&lt;/p&gt;
<?xml version="1.0" encoding="utf-8"?><feed xmlns="http://www.w3.org/2005/Atom" ><generator uri="https://jekyllrb.com/" version="4.0.0">Jekyll</generator><link href="https://galaxyproject.eu/feed.xml" rel="self" type="application/atom+xml" /><link href="https://galaxyproject.eu/" rel="alternate" type="text/html" /><updated>2023-12-12T02:52:24+01:00</updated><id>https://galaxyproject.eu/feed.xml</id><title type="html">Galaxy Europe</title><subtitle>The European Galaxy Instance</subtitle><entry><title type="html">UseGalaxy.eu Tool Updates for 2023-12-10</title><link href="https://galaxyproject.eu/posts/2023/12/10/tool-update/" rel="alternate" type="text/html" title="UseGalaxy.eu Tool Updates for 2023-12-10" /><published>2023-12-10T00:00:00+01:00</published><updated>2023-12-10T00:00:00+01:00</updated><id>https://galaxyproject.eu/posts/2023/12/10/tool-update</id><content type="html" xml:base="https://galaxyproject.eu/posts/2023/12/10/tool-update/">&lt;p&gt;On 2023-12-10, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in &lt;a href=&quot;https://build.galaxyproject.eu/job/usegalaxy-eu/job/install-tools/#422/&quot;&gt;Jenkins Build #422&lt;/a&gt;&lt;/p&gt;

&lt;h2 id=&quot;data-and-metadata-management&quot;&gt;Data and Metadata Management&lt;/h2&gt;

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27 changes: 18 additions & 9 deletions tools.html
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</div>

<div class="container" id="maincontainer">
<h1 id="european-galaxy-tools-3305-and-counting">European Galaxy tools (3305 and counting)</h1>
<h1 id="european-galaxy-tools-3314-and-counting">European Galaxy tools (3314 and counting)</h1>
<hr />

<h3>Get Data</h3>
Expand Down Expand Up @@ -339,7 +339,8 @@ <h3>Join, Subtract and Group</h3>
<hr />
<h2>Genomic File Manipulation</h2>
<h3>Convert Formats</h3>
<p><a href="https://usegalaxy.eu/root?tool_id=biom_convert" title="between BIOM table formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert</button></a>
<p><a href="https://usegalaxy.eu/root?tool_id=graphicsmagick_image_convert" title="with GraphicsMagick"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert image format</button></a>
<a href="https://usegalaxy.eu/root?tool_id=biom_convert" title="between BIOM table formats"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert</button></a>
<a href="https://usegalaxy.eu/root?tool_id=idpquery" title="Creates text reports from idpDB files."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">idpQuery</button></a>
<a href="https://usegalaxy.eu/root?tool_id=tab2fasta" title="converts tabular file to FASTA format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Tabular-to-FASTA</button></a>
<a href="https://usegalaxy.eu/root?tool_id=fasta2tab" title="converter"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FASTA-to-Tabular</button></a>
Expand All @@ -363,7 +364,6 @@ <h3>Convert Formats</h3>
<a href="https://usegalaxy.eu/root?tool_id=msms_extractor" title="Extract MS/MS scans from the mzML file(s) based on PSM report"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">msms_extractor</button></a>
<a href="https://usegalaxy.eu/root?tool_id=bax2bam" title="converts PacBio basecall format (bax.h5) into BAM"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">bax2bam</button></a>
<a href="https://usegalaxy.eu/root?tool_id=graphicsmagick_image_montage" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Image Montage</button></a>
<a href="https://usegalaxy.eu/root?tool_id=graphicsmagick_image_convert" title="with GraphicsMagick"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert image format</button></a>
<a href="https://usegalaxy.eu/root?tool_id=galaxy_intermine_exchange" title="Dataset"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Create InterMine Interchange</button></a>
<a href="https://usegalaxy.eu/root?tool_id=samtools_bam_to_cram" title="convert BAM alignments to CRAM format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">samtools BAM to CRAM</button></a>
<a href="https://usegalaxy.eu/root?tool_id=idconvert" title="Convert mass spectrometry identification files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">idconvert</button></a>
Expand Down Expand Up @@ -1200,7 +1200,8 @@ <h3>Genome editing</h3>
<h3>RNA-Seq</h3>
<p><a href="https://usegalaxy.eu/root?tool_id=blockbuster" title="detects blocks of overlapping reads using a gaussian-distribution approach"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">blockbuster</button></a></p>
<h3>RNA Analysis</h3>
<p><a href="https://usegalaxy.eu/root?tool_id=ribowaltz_plot" title="visual inspection of ribosome profiling data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">riboWaltz-plot</button></a>
<p><a href="https://usegalaxy.eu/root?tool_id=rbpbench" title="- Evaluate CLIP-seq and other genomic region data using a comprehensive collection of RBP binding motifs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">RBPBench</button></a>
<a href="https://usegalaxy.eu/root?tool_id=ribowaltz_plot" title="visual inspection of ribosome profiling data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">riboWaltz-plot</button></a>
<a href="https://usegalaxy.eu/root?tool_id=arriba" title="detect gene fusions from STAR aligned RNA-Seq data"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Arriba</button></a>
<a href="https://usegalaxy.eu/root?tool_id=filter_combined_via_tracking" title="using tracking file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Filter Combined Transcripts</button></a>
<a href="https://usegalaxy.eu/root?tool_id=express" title="Quantify the abundances of a set of target sequences from sampled subsequences"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">eXpress</button></a>
Expand Down Expand Up @@ -2264,8 +2265,12 @@ <h3>DNA Metabarcoding</h3>
<a href="https://usegalaxy.eu/root?tool_id=obi_ngsfilter" title="Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">NGSfilter</button></a>
<a href="https://usegalaxy.eu/root?tool_id=obi_illumina_pairend" title="Construct consensus reads from Illumina pair-end reads"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Illuminapairedend</button></a></p>
<h3>Data and Metadata Management</h3>
<p><a href="https://usegalaxy.eu/root?tool_id=makeeml" title="Create EML from EAL templates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make EML</button></a>
<a href="https://usegalaxy.eu/root?tool_id=eml2eal" title="Create EAL templates from EML metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EML to EAL</button></a></p>
<p><a href="https://usegalaxy.eu/root?tool_id=eal_templates" title="for core features of a data package for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make templates</button></a>
<a href="https://usegalaxy.eu/root?tool_id=makeeml" title="Create EML from EAL templates"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make EML</button></a>
<a href="https://usegalaxy.eu/root?tool_id=eml2eal" title="Create EAL templates from EML metadata"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">EML to EAL</button></a>
<a href="https://usegalaxy.eu/root?tool_id=eal_table_template" title="attributes and categorical variables for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make templates for data tables</button></a>
<a href="https://usegalaxy.eu/root?tool_id=geo_cov_template" title="for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make geographic coverage template</button></a>
<a href="https://usegalaxy.eu/root?tool_id=taxo_cov_template" title="for EML metadata creation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Make taxonomic coverage template</button></a></p>
<h3>Virology</h3>
<p><a href="https://usegalaxy.eu/root?tool_id=ivar_consensus" title="Call consensus from aligned BAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ivar consensus</button></a>
<a href="https://usegalaxy.eu/root?tool_id=ivar_removereads" title="Remove reads from trimmed BAM file"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">ivar removereads</button></a>
Expand Down Expand Up @@ -2570,9 +2575,9 @@ <h3>Proteomics</h3>
<a href="https://usegalaxy.eu/root?tool_id=eggnog_mapper_annotate" title="annotation phase"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">eggNOG Mapper</button></a>
<a href="https://usegalaxy.eu/root?tool_id=eggnog_mapper_search" title="search phase"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">eggNOG Mapper</button></a></p>
<h3>Metabolomics</h3>
<p><a href="https://usegalaxy.eu/root?tool_id=matchms_metadata_merge" title="Merge metadata csv into MSP by a specified column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms metadata merge</button></a>
<p><a href="https://usegalaxy.eu/root?tool_id=matchms_formatter" title="reformat scores object of matchms to long format table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms scores formatter</button></a>
<a href="https://usegalaxy.eu/root?tool_id=matchms_metadata_merge" title="Merge metadata csv into MSP by a specified column"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms metadata merge</button></a>
<a href="https://usegalaxy.eu/root?tool_id=matchms_metadata_export" title="extract all metadata from mass spectra file to tabular format"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms metadata export</button></a>
<a href="https://usegalaxy.eu/root?tool_id=matchms_formatter" title="reformat scores object of matchms to long format table"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms scores formatter</button></a>
<a href="https://usegalaxy.eu/root?tool_id=Transformation" title="Transforms the dataMatrix intensity values"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Transformation</button></a>
<a href="https://usegalaxy.eu/root?tool_id=abims_anova" title="N-way anova. With ou Without interactions"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Anova</button></a>
<a href="https://usegalaxy.eu/root?tool_id=Multivariate" title="PCA, PLS and OPLS"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Multivariate</button></a>
Expand Down Expand Up @@ -2653,6 +2658,8 @@ <h3>Metabolomics</h3>
<a href="https://usegalaxy.eu/root?tool_id=matchms_networking" title="create similarity network graph from matchms similarity scores"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms networking</button></a>
<a href="https://usegalaxy.eu/root?tool_id=matchms_spectral_similarity" title="matchms spectral similarity calculation"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms spectral similarity</button></a>
<a href="https://usegalaxy.eu/root?tool_id=matchms_subsetting" title="Extract spectra from a library given unique metadata identifier"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms subsetting</button></a>
<a href="https://usegalaxy.eu/root?tool_id=matchms_add_key" title="Set metadata key in MSP to static value"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms add key</button></a>
<a href="https://usegalaxy.eu/root?tool_id=matchms_remove_key" title="Remove metadata entry for all spectra in a library"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms remove key</button></a>
<a href="https://usegalaxy.eu/root?tool_id=matchms_split" title="split a large library into subsets"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">matchms split library</button></a>
<a href="https://usegalaxy.eu/root?tool_id=abims_xcms_refine" title="Remove or merge chromatographic peaks based on specific criteria."><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">xcms refineChromPeaks (refine)</button></a>
<a href="https://usegalaxy.eu/root?tool_id=isoplot" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Isoplot: Generate plots from isocor output</button></a>
Expand Down Expand Up @@ -2767,6 +2774,7 @@ <h3>ChemicalToolBox</h3>
<a href="https://usegalaxy.eu/root?tool_id=ctb_im_xcos" title="scoring"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">XCos</button></a>
<a href="https://usegalaxy.eu/root?tool_id=featurestein" title="feature overlay scoring"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">‘FeatureStein’ fragment overlay scoring</button></a>
<a href="https://usegalaxy.eu/root?tool_id=gmx_merge_topology_files" title="and GRO files"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Merge GROMACS topologies</button></a>
<a href="https://usegalaxy.eu/root?tool_id=rem_complex" title="Remove molecular coordination complexes from a list of structure representations"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Remove coordination complexes</button></a>
<a href="https://usegalaxy.eu/root?tool_id=openduck_chunk" title="for dynamic undocking"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">OpenDUck chunk</button></a>
<a href="https://usegalaxy.eu/root?tool_id=openduck_run_smd" title="steered molecular dynamics runs"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Run OpenDUck</button></a>
<a href="https://usegalaxy.eu/root?tool_id=xchem_transfs_scoring" title="using deep learning"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">XChem TransFS pose scoring</button></a>
Expand Down Expand Up @@ -3112,7 +3120,8 @@ <h3>Apollo</h3>
<a href="https://usegalaxy.eu/root?tool_id=delete_organism" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delete an Apollo record</button></a>
<a href="https://usegalaxy.eu/root?tool_id=delete_features" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Delete all annotations from an Apollo record</button></a></p>
<h3>Imaging</h3>
<p><a href="https://usegalaxy.eu/root?tool_id=ip_binary_to_labelimage" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert binary image to label map</button></a>
<p><a href="https://usegalaxy.eu/root?tool_id=bia_download" title="Download images from Bioimage Archive"><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">FTP Link for Bioimage Archive</button></a>
<a href="https://usegalaxy.eu/root?tool_id=ip_binary_to_labelimage" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Convert binary image to label map</button></a>
<a href="https://usegalaxy.eu/root?tool_id=ip_curve_fitting" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform curve fitting</button></a>
<a href="https://usegalaxy.eu/root?tool_id=ip_image_registration" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform affine image registration (intensity-based)</button></a>
<a href="https://usegalaxy.eu/root?tool_id=ip_landmark_registration" title=""><button type="button" class="btn btn-outline-primary btn-rounded waves-effect btn-xs" style="margin: 2px">Perform affine image registration (landmark-based)</button></a>
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