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Merge branch 'main' into get-first-commit-of-suite
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@paulzierep
paulzierep authored Oct 8, 2024
2 parents 9401d10 + 7839085 commit f240f16
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Showing 5 changed files with 46 additions and 15 deletions.
38 changes: 26 additions & 12 deletions communities/all/resources/test_tools.json
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Expand Up @@ -98,7 +98,11 @@
"No. of tool users (5 years) (usegalaxy.org.au)": 305,
"No. of tool users (all time) (usegalaxy.org.au)": 305,
"Tool usage (5 years) (usegalaxy.org.au)": 11,
"Tool usage (all time) (usegalaxy.org.au)": 11
"Tool usage (all time) (usegalaxy.org.au)": 11,
"No. of tool users (5 years) - all main servers": 1739,
"No. of tool users (all time) - all main servers": 7051,
"Tool usage (5 years) - all main servers": 131,
"Tool usage (all time) - all main servers": 133
},
{
"Galaxy wrapper id": "abritamr",
Expand Down Expand Up @@ -179,7 +183,11 @@
"No. of tool users (5 years) (usegalaxy.org.au)": 0,
"No. of tool users (all time) (usegalaxy.org.au)": 0,
"Tool usage (5 years) (usegalaxy.org.au)": 0,
"Tool usage (all time) (usegalaxy.org.au)": 0
"Tool usage (all time) (usegalaxy.org.au)": 0,
"No. of tool users (5 years) - all main servers": 1139,
"No. of tool users (all time) - all main servers": 1139,
"Tool usage (5 years) - all main servers": 109,
"Tool usage (all time) - all main servers": 109
},
{
"Galaxy wrapper id": "aldex2",
Expand Down Expand Up @@ -272,7 +280,11 @@
"No. of tool users (5 years) (usegalaxy.org.au)": 0,
"No. of tool users (all time) (usegalaxy.org.au)": 0,
"Tool usage (5 years) (usegalaxy.org.au)": 0,
"Tool usage (all time) (usegalaxy.org.au)": 0
"Tool usage (all time) (usegalaxy.org.au)": 0,
"No. of tool users (5 years) - all main servers": 262,
"No. of tool users (all time) - all main servers": 262,
"Tool usage (5 years) - all main servers": 36,
"Tool usage (all time) - all main servers": 36
},
{
"Galaxy wrapper id": "fastp",
Expand Down Expand Up @@ -365,7 +377,11 @@
"No. of tool users (5 years) (usegalaxy.org.au)": 76462,
"No. of tool users (all time) (usegalaxy.org.au)": 76462,
"Tool usage (5 years) (usegalaxy.org.au)": 2242,
"Tool usage (all time) (usegalaxy.org.au)": 2242
"Tool usage (all time) (usegalaxy.org.au)": 2242,
"No. of tool users (5 years) - all main servers": 1624807,
"No. of tool users (all time) - all main servers": 1625832,
"Tool usage (5 years) - all main servers": 19811,
"Tool usage (all time) - all main servers": 19873
},
{
"Galaxy wrapper id": "spades",
Expand All @@ -384,14 +400,8 @@
"bio.tool id": "spades",
"bio.tool ids": [
"metaplasmidspades",
"rnaspades",
"metaviralspades",
"spades",
"rnaviralspades",
"plasmidspades",
"coronaspades",
"biosyntheticspades",
"metaspades"
"rnaspades",
],
"biii": null,
"bio.tool name": "SPAdes",
Expand Down Expand Up @@ -474,6 +484,10 @@
"No. of tool users (5 years) (usegalaxy.org.au)": 54067,
"No. of tool users (all time) (usegalaxy.org.au)": 61541,
"Tool usage (5 years) (usegalaxy.org.au)": 5817,
"Tool usage (all time) (usegalaxy.org.au)": 6653
"Tool usage (all time) (usegalaxy.org.au)": 6653,
"No. of tool users (5 years) - all main servers": 257254,
"No. of tool users (all time) - all main servers": 269129,
"Tool usage (5 years) - all main servers": 28813,
"Tool usage (all time) - all main servers": 29969
}
]
1 change: 1 addition & 0 deletions communities/all/resources/test_tools.tsv
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Expand Up @@ -4,3 +4,4 @@ abritamr abritamr A pipeline for running AMRfinderPlus and collating results int
aldex2 aldex2 Performs analysis Of differential abundance taking sample variation into account aldex2 aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. Statistical inference Gene expression, Statistics and probability To update https://github.com/ggloor/ALDEx_bioc Metagenomics aldex2 2024-03-01 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/aldex2 1.26.0 bioconductor-aldex2 1.34.0 Statistical inference Gene expression, Statistics and probability 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 262 262 36 36 0 0 0 0 0 0 0 0
fastp fastp Fast all-in-one preprocessing for FASTQ files fastp fastp fastp A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. Sequencing quality control, Sequence contamination filtering Sequence analysis, Probes and primers To update https://github.com/OpenGene/fastp Sequence Analysis fastp 2024-03-11 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/fastp fastp 0.23.4 Sequence contamination filtering Probes and primers 1 1 1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 1 0 0 0 1 0 0 0 0 0 0 1 1 1 1 1126086 1127111 6847 6909 422259 422259 10722 10722 76462 76462 2242 2242
spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades 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. spades metaplasmidspades, rnaspades, metaviralspades, spades, rnaviralspades, plasmidspades, coronaspades, biosyntheticspades, metaspades SPAdes 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. Genome assembly Sequence assembly To update https://github.com/ablab/spades Assembly, RNA, Metagenomics spades 2024-03-12 iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/spades 3.15.5 spades 4.0.0 Genome assembly Sequence assembly 9 9 9 0 9 9 9 0 0 0 0 0 0 0 0 0 0 0 0 0 1 3 8 0 0 2 0 0 0 3 0 0 0 0 0 0 3 9 3 0 82716 87113 8209 8526 120471 120475 14787 14790 54067 61541 5817 6653

16 changes: 16 additions & 0 deletions sources/bin/extract_galaxy_tools.py
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Expand Up @@ -62,6 +62,14 @@
"Tool usage (all time) (usegalaxy.org.au)": usage_stats_path.joinpath("org.au/tool_users_until_2024.08.31.csv"),
}

# all columns that contain the text will be summed up to a new column with summed up stats
GALAXY_TOOL_STATS_SUM = [
"No. of tool users (5 years)",
"No. of tool users (all time)",
"Tool usage (5 years)",
"Tool usage (all time)",
]

# load the configs globally
with open(conf_path) as f:
configs = yaml.safe_load(f)
Expand Down Expand Up @@ -685,6 +693,14 @@ def get_tools(repo_list: list, edam_ontology: dict) -> List[Dict]:
tool_stats_df = pd.read_csv(path)
tool[name] = get_tool_stats_from_stats_file(tool_stats_df, tool["Galaxy tool ids"])

# sum up tool stats
for names_to_match in GALAXY_TOOL_STATS_SUM:
summed_stat = 0
for col_name in tool.keys():
if names_to_match in col_name:
summed_stat += tool[col_name]
tool[f"{names_to_match} - all main servers"] = summed_stat

return tools


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2 changes: 1 addition & 1 deletion sources/bin/format_tools.sh
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Expand Up @@ -8,6 +8,6 @@ python sources/bin/create_interactive_table.py \
python sources/bin/create_wordcloud.py \
--input "communities/all/resources/tools.tsv" \
--name-col "Galaxy wrapper id" \
--stat-col "No. of tool users (2022-2023) (usegalaxy.eu)" \
--stat-col "No. of tool users (5 years) - all main servers" \
--wordcloud_mask "sources/data/usage_stats/wordcloud_mask.png" \
--output "communities/all/resources/tools_wordcloud.png" \
4 changes: 2 additions & 2 deletions sources/bin/get_community_tools.sh
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Expand Up @@ -23,7 +23,7 @@ if [[ ! -z $1 && $1 == "test" ]]; then
python sources/bin/create_wordcloud.py \
--input "communities/microgalaxy/resources/tools.tsv" \
--name-col "Galaxy wrapper id" \
--stat-col "No. of tool users (2022-2023) (usegalaxy.eu)" \
--stat-col "No. of tool users (5 years) - all main servers" \
--wordcloud_mask "sources/data/usage_stats/wordcloud_mask.png" \
--output "communities/microgalaxy/resources/tools_wordcloud.png"

Expand Down Expand Up @@ -57,7 +57,7 @@ else
python sources/bin/create_wordcloud.py \
--input "communities/$community/resources/tools.tsv" \
--name-col "Galaxy wrapper id" \
--stat-col "No. of tool users (2022-2023) (usegalaxy.eu)" \
--stat-col "No. of tool users (5 years) - all main servers" \
--wordcloud_mask "sources/data/usage_stats/wordcloud_mask.png" \
--output "communities/$community/resources/tools_wordcloud.png"
fi;
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