fetch all tools bot - step fetch

galaxyproject · Jun 25, 2024 · 627ca72 · 627ca72
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commit 627ca72
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Showing 2 changed files with 47 additions and 47 deletions.
diff --git a/results/repositories03.list_tools.json b/results/repositories03.list_tools.json
@@ -189,7 +189,7 @@
         "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr",
         "Galaxy wrapper version": "1.0.14",
         "Conda id": "abritamr",
-        "Conda version": "1.0.17",
+        "Conda version": "1.0.18",
         "EDAM operation (no superclasses)": [
             "Antimicrobial resistance prediction"
         ],
@@ -1196,7 +1196,7 @@
             "Annotation"
         ],
         "EDAM topic": [],
-        "Status": "Up-to-date",
+        "Status": "To update",
         "Source": "https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids",
         "ToolShed categories": [
             "Genome annotation"
@@ -1207,7 +1207,7 @@
         "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids",
         "Galaxy wrapper version": "3.18.0",
         "Conda id": "bioconductor-org.hs.eg.db",
-        "Conda version": "3.18.0",
+        "Conda version": null,
         "EDAM operation (no superclasses)": [
             "Annotation"
         ],
@@ -1513,7 +1513,7 @@
         "bio.tool description": null,
         "EDAM operation": [],
         "EDAM topic": [],
-        "Status": "Up-to-date",
+        "Status": "To update",
         "Source": "https://github.com/rjchallis/assembly-stats",
         "ToolShed categories": [
             "Assembly"
@@ -1524,7 +1524,7 @@
         "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats",
         "Galaxy wrapper version": "17.02",
         "Conda id": "rjchallis-assembly-stats",
-        "Conda version": "17.02",
+        "Conda version": null,
         "EDAM operation (no superclasses)": [],
         "EDAM topic (no superclasses)": [],
         "Available on UseGalaxy.org (Main)": 0,
@@ -1770,7 +1770,7 @@
             "Data submission, annotation and curation",
             "Sequence analysis"
         ],
-        "Status": "Up-to-date",
+        "Status": "To update",
         "Source": "https://github.com/oschwengers/bakta",
         "ToolShed categories": [
             "Sequence Analysis"
@@ -1781,7 +1781,7 @@
         "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta",
         "Galaxy wrapper version": "1.9.3",
         "Conda id": "bakta",
-        "Conda version": "1.9.3",
+        "Conda version": null,
         "EDAM operation (no superclasses)": [
             "Genome annotation"
         ],
@@ -2334,7 +2334,7 @@
         "bio.tool description": null,
         "EDAM operation": [],
         "EDAM topic": [],
-        "Status": "Up-to-date",
+        "Status": "To update",
         "Source": "https://github.com/seqan/anise_basil",
         "ToolShed categories": [
             "Variant Analysis"
@@ -2345,7 +2345,7 @@
         "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil",
         "Galaxy wrapper version": "1.2.0",
         "Conda id": "anise_basil",
-        "Conda version": "1.2.0",
+        "Conda version": null,
         "EDAM operation (no superclasses)": [],
         "EDAM topic (no superclasses)": [],
         "Available on UseGalaxy.org (Main)": 1,
@@ -2645,8 +2645,8 @@
         "Description": "BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.",
         "bio.tool id": "bbmap",
         "bio.tool ids": [
-            "bbmap",
-            "bbtools"
+            "bbtools",
+            "bbmap"
         ],
         "biii": null,
         "bio.tool name": "BBMap",
@@ -3057,7 +3057,7 @@
         "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle",
         "Galaxy wrapper version": "5.2_21Apr21.304",
         "Conda id": "beagle",
-        "Conda version": "5.4_22Jul22.46e",
+        "Conda version": null,
         "EDAM operation (no superclasses)": [],
         "EDAM topic (no superclasses)": [],
         "Available on UseGalaxy.org (Main)": 0,
@@ -3381,7 +3381,7 @@
         "bio.tool description": null,
         "EDAM operation": [],
         "EDAM topic": [],
-        "Status": "Up-to-date",
+        "Status": "To update",
         "Source": "https://github.com/tseemann/berokka",
         "ToolShed categories": [
             "Fasta Manipulation"
@@ -3392,7 +3392,7 @@
         "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka",
         "Galaxy wrapper version": "0.2.3",
         "Conda id": "berokka",
-        "Conda version": "0.2.3",
+        "Conda version": null,
         "EDAM operation (no superclasses)": [],
         "EDAM topic (no superclasses)": [],
         "Available on UseGalaxy.org (Main)": 0,
@@ -3958,7 +3958,7 @@
         "bio.tool description": null,
         "EDAM operation": [],
         "EDAM topic": [],
-        "Status": "Up-to-date",
+        "Status": "To update",
         "Source": "https://github.com/institut-de-genomique/biscot",
         "ToolShed categories": [
             "Assembly"
@@ -3969,7 +3969,7 @@
         "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot",
         "Galaxy wrapper version": "2.3.3",
         "Conda id": "biscot",
-        "Conda version": "2.3.3",
+        "Conda version": null,
         "EDAM operation (no superclasses)": [],
         "EDAM topic (no superclasses)": [],
         "Available on UseGalaxy.org (Main)": 0,
@@ -4194,7 +4194,7 @@
         "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2",
         "Galaxy wrapper version": "2.5.3",
         "Conda id": "bowtie2",
-        "Conda version": "2.5.4",
+        "Conda version": null,
         "EDAM operation (no superclasses)": [
             "Read mapping"
         ],
@@ -7404,11 +7404,11 @@
             "Transcriptomics",
             "Sequence analysis"
         ],
-        "Available on UseGalaxy.org (Main)": 0,
+        "Available on UseGalaxy.org (Main)": 1,
         "Available on UseGalaxy.org.au": 0,
         "Available on UseGalaxy.eu": 1,
         "Available on UseGalaxy.fr": 1,
-        "Tools available on UseGalaxy.org (Main)": 0,
+        "Tools available on UseGalaxy.org (Main)": 1,
         "Tools available on UseGalaxy.org.au": 0,
         "Tools available on UseGalaxy.eu": 1,
         "Tools available on UseGalaxy.fr": 1,
@@ -16063,8 +16063,8 @@
         "Description": "An algorithm for identification of the optimal scoring subnetwork.",
         "bio.tool id": "heinz",
         "bio.tool ids": [
-            "bionet",
-            "heinz"
+            "heinz",
+            "bionet"
         ],
         "biii": null,
         "bio.tool name": "Heinz",
@@ -17070,7 +17070,7 @@
         "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper",
         "Galaxy wrapper version": "2.1.6",
         "Conda id": "hybpiper",
-        "Conda version": "2.1.7",
+        "Conda version": "2.1.8",
         "EDAM operation (no superclasses)": [
             "Sequence trimming",
             "Sequence assembly",
@@ -26653,7 +26653,7 @@
         "Galaxy wrapper parsed folder": "https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil",
         "Galaxy wrapper version": "3.1.1",
         "Conda id": "nonpareil",
-        "Conda version": "3.4.1",
+        "Conda version": "3.5.1",
         "EDAM operation (no superclasses)": [
             "Operation"
         ],
@@ -31266,8 +31266,8 @@
         "Description": "QIIME to perform microbial community analysis",
         "bio.tool id": "qiime_add_on",
         "bio.tool ids": [
-            "qiime_core",
-            "qiime_add_on"
+            "qiime_add_on",
+            "qiime_core"
         ],
         "biii": null,
         "bio.tool name": "qiime_add_on",
@@ -38183,14 +38183,14 @@
         "bio.tool id": "spades",
         "bio.tool ids": [
             "rnaspades",
-            "metaviralspades",
-            "rnaviralspades",
             "spades",
+            "biosyntheticspades",
             "metaspades",
-            "metaplasmidspades",
+            "rnaviralspades",
             "plasmidspades",
             "coronaspades",
-            "biosyntheticspades"
+            "metaviralspades",
+            "metaplasmidspades"
         ],
         "biii": null,
         "bio.tool name": "SPAdes",
@@ -44754,7 +44754,7 @@
         "Tools available on GASLINI": 0,
         "Tools available on Galaxy@AuBi": 0,
         "Tools available on Galaxy@Pasteur": 0,
-        "Tools available on GalaxyTrakr": 0,
+        "Tools available on GalaxyTrakr": 1,
         "Tools available on Genomic Hyperbrowser": 0,
         "Tools available on GigaGalaxy": 0,
         "Tools available on HyPhy HIV NGS Tools": 0,