From 73f96afabca939d3924f0cdea80596e535577044 Mon Sep 17 00:00:00 2001 From: github-actions Date: Tue, 5 Mar 2024 09:22:26 +0000 Subject: [PATCH] fetch all tools bot - step filter --- results/imaging/index.html | 116 ++++---- results/microgalaxy/index.html | 488 ++++++++++++++++----------------- 2 files changed, 302 insertions(+), 302 deletions(-) diff --git a/results/imaging/index.html b/results/imaging/index.html index da2e3606..eea7eb6c 100644 --- a/results/imaging/index.html +++ b/results/imaging/index.html @@ -56,6 +56,7 @@ + @@ -80,11 +81,11 @@ - + @@ -109,9 +110,9 @@ - + @@ -136,9 +137,9 @@ - + @@ -163,9 +164,9 @@ - + @@ -190,9 +191,9 @@ - + @@ -217,9 +218,9 @@ - + @@ -244,9 +245,9 @@ - + @@ -271,9 +272,9 @@ - + @@ -298,9 +299,9 @@ - + @@ -325,9 +326,9 @@ - + @@ -352,9 +353,9 @@ - + @@ -379,9 +380,9 @@ - + @@ -406,9 +407,9 @@ - + @@ -433,9 +434,9 @@ - + @@ -460,9 +461,9 @@ - + @@ -487,9 +488,9 @@ - + @@ -514,9 +515,9 @@ - + @@ -541,9 +542,9 @@ - + @@ -568,9 +569,9 @@ - + @@ -595,9 +596,9 @@ - + @@ -622,9 +623,9 @@ - + @@ -649,9 +650,9 @@ - + @@ -676,9 +677,9 @@ - + @@ -703,9 +704,9 @@ - + @@ -730,9 +731,9 @@ - + @@ -757,9 +758,9 @@ - + @@ -784,9 +785,9 @@ - + @@ -811,9 +812,9 @@ - + @@ -838,9 +839,9 @@ - + @@ -865,9 +866,9 @@ - + @@ -892,9 +893,9 @@ - + @@ -919,9 +920,9 @@ - + @@ -946,9 +947,9 @@ - + @@ -973,9 +974,9 @@ - + @@ -1000,9 +1001,9 @@ - + @@ -1027,9 +1028,9 @@ - + @@ -1054,9 +1055,9 @@ - + @@ -1081,9 +1082,9 @@ - + @@ -1108,9 +1109,9 @@ - + @@ -1135,9 +1136,9 @@ - + @@ -1162,9 +1163,9 @@ - + @@ -1189,9 +1190,9 @@ - + @@ -1216,9 +1217,9 @@ - + @@ -1243,9 +1244,9 @@ - + @@ -1270,9 +1271,9 @@ - + @@ -1297,9 +1298,9 @@ - + @@ -1324,9 +1325,9 @@ - + @@ -1351,9 +1352,9 @@ - + @@ -1378,9 +1379,9 @@ - + @@ -1405,9 +1406,9 @@ - + @@ -1432,9 +1433,9 @@ - + @@ -1459,9 +1460,9 @@ - + @@ -1486,9 +1487,9 @@ - + @@ -1513,9 +1514,9 @@ - + @@ -1540,9 +1541,9 @@ - + @@ -1567,9 +1568,9 @@ - + @@ -1594,9 +1595,9 @@ - + @@ -1621,7 +1622,6 @@ -
Expand Galaxy wrapper id Total tool usage (usegalaxy.eu) No. of tool users (2022-2023) (usegalaxy.eu)https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.euExpand
2d_auto_threshold 6541.0 39.0(0/1) (1/1) (1/1)
2d_feature_extraction 13760.0 19.0(0/1) (1/1) (1/1)
2d_filter_segmentation_by_features 6834.0 18.0(0/1) (1/1) (1/1)
2d_histogram_equalization 656.0 39.0(0/1) (1/1) (1/1)
2d_simple_filter 6156.0 35.0(0/1) (1/1) (1/1)
3d_tensor_feature_dimension_reduction (0/1) (0/1) (0/1)
anisotropic_diffusion 40.0 (0/1) (0/1) (1/1)
bfconvert 1523.0 38.0(0/1) (1/1) (1/1)
binary2labelimage 1273.0 34.0(0/1) (1/1) (1/1)
binaryimage2points 29.0 (0/1) (0/1) (1/1)
bioformats2raw 9.0 (0/1) (0/1) (1/1)
color-deconvolution (0/1) (0/1) (1/1)
concat_channels 78.0 3.0(0/1) (0/1) (1/1)
coordinates_of_roi 16546.0 8.0(0/1) (0/1) (1/1)
count_objects 272.0 25.0(0/1) (1/1) (1/1)
curve_fitting 12.0 1.0(0/1) (0/1) (1/1)
detection_viz 46.0 2.0(0/1) (0/1) (1/1)
image_info 621.0 41.0(0/1) (1/1) (1/1)
image_registration_affine 12.0 2.0(0/1) (0/1) (1/1)
imagecoordinates_flipaxis 21825.0 7.0(0/1) (0/1) (1/1)
labelimage2points 36.0 (0/1) (0/1) (1/1)
landmark_registration 857.0 9.0(1/1) (0/1) (1/1)
mahotas-features (0/1) (0/1) (1/1)
mergeneighboursinlabelimage 25.0 (0/1) (0/1) (1/1)
overlay_images 60.0 21.0(0/1) (0/1) (1/1)
permutate_axis 42.0 (0/1) (0/1) (1/1)
points2binaryimage 41.0 2.0(0/1) (0/1) (1/1)
points2labelimage 66.0 (0/1) (0/1) (1/1)
points_association_nn 29.0 2.0(0/1) (0/1) (1/1)
projective_transformation 44.0 1.0(0/1) (0/1) (1/1)
projective_transformation_points 21208.0 9.0(0/1) (0/1) (1/1)
rfove 7.0 (0/1) (0/1) (1/1)
scale_image 615.0 9.0(0/1) (0/1) (1/1)
segmetrics 3.0 2.0(0/1) (0/1) (1/1)
slice_image 102.0 (0/1) (0/1) (1/1)
split_labelmap 42.0 (0/1) (0/1) (1/1)
spot_detection_2d 16.0 3.0(0/1) (0/1) (1/1)
superdsm 16.0 2.0(0/1) (0/1) (1/1)
visceral-evaluatesegmentation (0/1) (0/1) (1/1)
wsi_extract_top_view 38.0 (0/1) (0/1) (1/1)
cellpose (0/1) (0/1) (1/1)
cellprofiler (0/23) (23/23) (23/23)
cellprofiler_v4 (0/1) (0/1) (1/1)
bia-ftplinks (0/1) (0/1) (1/1)
graphicsmagick (1/3) (0/3) (3/3)
imagej2 (0/27) (0/27) (27/27)
woundhealing (0/1) (0/1) (1/1)
spyboat 67.0 1.0(0/1) (0/1) (1/1)
qupath_roi_splitter 59.0 5.0(0/1) (0/1) (1/1)
hyperstack_to_bleach_corrected_movie (0/1) (0/1) (0/1)
incucyte_stack_and_upload_omero (0/1) (0/1) (0/1)
measure_gastruloids (0/1) (0/1) (0/1)
omero_clean_rois_tables (0/1) (0/1) (0/1)
omero_get_children_ids (0/1) (0/1) (0/1)
omero_hyperstack_to_fluo_measurements_on_gastruloid (0/1) (0/1) (0/1)
omero_hyperstack_to_gastruloid_measurements (0/1) (0/1) (0/1)
upload_roi_and_measures_to_omero (0/1) (0/1) (0/1)
diff --git a/results/microgalaxy/index.html b/results/microgalaxy/index.html index 4584e790..df4b7725 100644 --- a/results/microgalaxy/index.html +++ b/results/microgalaxy/index.html @@ -56,6 +56,7 @@ + @@ -80,11 +81,11 @@ - + @@ -109,9 +110,9 @@ - + @@ -136,9 +137,9 @@ - + @@ -163,9 +164,9 @@ - + @@ -190,9 +191,9 @@ - + @@ -217,9 +218,9 @@ - + @@ -244,9 +245,9 @@ - + @@ -271,9 +272,9 @@ - + @@ -298,9 +299,9 @@ - + @@ -325,9 +326,9 @@ - + @@ -352,9 +353,9 @@ - + @@ -379,9 +380,9 @@ - + @@ -406,9 +407,9 @@ - + @@ -433,9 +434,9 @@ - + @@ -460,9 +461,9 @@ - + @@ -487,9 +488,9 @@ - + @@ -514,9 +515,9 @@ - + @@ -541,9 +542,9 @@ - + @@ -568,9 +569,9 @@ - + @@ -595,9 +596,9 @@ - + @@ -622,9 +623,9 @@ - + @@ -649,9 +650,9 @@ - + @@ -676,9 +677,9 @@ - + @@ -703,9 +704,9 @@ - + @@ -730,9 +731,9 @@ - + @@ -757,9 +758,9 @@ - + @@ -784,9 +785,9 @@ - + @@ -811,9 +812,9 @@ - + @@ -838,9 +839,9 @@ - + @@ -865,9 +866,9 @@ - + @@ -892,9 +893,9 @@ - + @@ -919,9 +920,9 @@ - + @@ -946,9 +947,9 @@ - + @@ -973,9 +974,9 @@ - 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Expand Galaxy wrapper id Total tool usage (usegalaxy.eu) No. of tool users (2022-2023) (usegalaxy.eu)https://usegalaxy.org https://usegalaxy.org.au https://usegalaxy.euExpand
TreeBest (0/1) (0/1) (1/1)
ete 1255.0 67.0(0/7) (0/7) (7/7)
lotus2 936.0 114.0(0/1) (0/1) (1/1)
abacas (0/1) (0/1) (0/1)
assemblystats (0/1) (0/1) (0/1)
biohansel (0/1) (0/1) (0/1)
combine_assembly_stats (0/1) (0/1) (0/1)
cryptogenotyper 8518.0 16.0(0/1) (0/1) (1/1)
ectyper 9907.0 53.0(0/1) (0/1) (1/1)
filter_spades_repeats (0/1) (0/1) (0/1)
getmlst (0/1) (0/1) (0/1)
hivtrace (0/1) (0/1) (0/1)
kat_filter (0/1) (0/1) (0/1)
mob_suite 89021.0 322.0(0/2) (2/2) (2/2)
mrbayes (0/1) (0/1) (0/1)
mykrobe_parser (0/1) (0/1) (0/1)
plasmidspades (0/1) (0/1) (0/1)
promer (0/1) (0/1) (0/1)
sistr_cmd 2489.0 133.0(0/1) (1/1) (1/1)
smalt (0/1) (0/1) (0/1)
srst2 205.0 22.0(0/1) (0/1) (1/1)
staramr 12673.0 889.0(1/1) (1/1) (1/1)
stringmlst (0/1) (0/1) (0/1)
repeatexplorer2 (0/1) (0/1) (1/1)
cd_hit_dup (1/1) (0/1) (0/1)
multispecies_orthologous_microsats (0/1) (0/1) (0/1)
quality_filter (0/1) (0/1) (0/1)
gi2taxonomy 660.0 27.0(0/1) (0/1) (1/1)
kraken2tax 14683.0 481.0(1/1) (1/1) (1/1)
lca_wrapper 137.0 2.0(0/1) (0/1) (1/1)
t2ps 457.0 31.0(0/1) (0/1) (1/1)
t2t_report 947.0 26.0(0/1) (0/1) (1/1)
antismash 14596.0 279.0(1/1) (1/1) (1/1)
combine_metaphlan_humann (0/1) (0/1) (1/1)
compare_humann2_output 332.0 10.0(0/1) (0/1) (0/1)
flye 20904.0 1499.0(1/1) (1/1) (1/1)
format_metaphlan2_output 5588.0 166.0(0/1) (0/1) (1/1)
glimmer_hmm (0/1) (0/1) (0/1)
graphmap (0/2) (0/2) (2/2)
iprscan5 (0/1) (0/1) (0/1)
itsx 868.0 38.0(0/1) (0/1) (1/1)
lighter 152.0 9.0(0/1) (0/1) (1/1)
mafft 143045.0 817.0(2/2) (2/2) (2/2)
mcl 29.0 10.0(0/1) (0/1) (0/1)
minipolish 185.0 21.0(0/1) (0/1) (1/1)
nextdenovo 268.0 84.0(0/1) (0/1) (1/1)
nucleosome_prediction 861.0 2.0(0/1) (0/1) (1/1)
pfamscan 165.0 19.0(1/1) (1/1) (1/1)
racon 21353.0 309.0(1/1) (1/1) (1/1)
infernal 100230.0 67.0(0/6) (6/6) (6/6)
rRNA (0/1) (0/1) (0/1)
rbpbench 36.0 (0/1) (0/1) (1/1)
reago (0/1) (0/1) (0/1)
sortmerna 18504.0 376.0(1/1) (1/1) (1/1)
salmon 55161.0 746.0(2/3) (1/3) (3/3)
tapscan (0/1) (0/1) (1/1)
trim_galore 238699.0 2334.0(1/1) (1/1) (1/1)
wtdbg 1660.0 116.0(0/1) (0/1) (1/1)
clinod (1/1) (0/1) (0/1)
effectiveT3 (0/1) (0/1) (0/1)
abricate 496717.0 1764.0(3/3) (3/3) (3/3)
abritamr (0/1) (0/1) (0/1)
abyss 4278.0 391.0(0/1) (1/1) (1/1)
aldex2 129.0 13.0(0/1) (0/1) (1/1)
amplican 53.0 12.0(0/1) (0/1) (1/1)
amrfinderplus 591.0 (0/1) (0/1) (1/1)
ancombc 7.0 4.0(0/1) (0/1) (1/1)
artic (0/2) (0/2) (2/2)
bakta 2982.0 151.0(0/1) (1/1) (1/1)
bandage 44390.0 2016.0(2/2) (2/2) (2/2)
bayescan 64.0 8.0(0/1) (0/1) (1/1)
bigscape (0/1) (0/1) (0/1)
binning_refiner 81.0 21.0(0/1) (0/1) (1/1)
biom_format (2/6) (2/6) (1/6)
bracken 18351.0 326.0(0/1) (0/1) (1/1)
busco 86180.0 1804.0(1/1) (1/1) (1/1)
cactus (0/2) (2/2) (2/2)
cat (5/5) (2/5) (5/5)
cdhit 8278.0 6.0(0/1) (0/1) (1/1)
cemitool 98.0 9.0(1/1) (0/1) (1/1)
checkm (0/10) (0/10) (10/10)
clustalw 46793.0 651.0(1/1) (1/1) (1/1)
codeml 60901.0 29.0(0/1) (0/1) (1/1)
cojac (2/3) (0/3) (3/3)
compleasm (0/1) (0/1) (1/1)
concoct 250.0 29.0(0/5) (0/5) (5/5)
coverm (0/2) (0/2) (2/2)
cutadapt 232004.0 5090.0(1/1) (1/1) (1/1)
dada2 (10/10) (10/10) (10/10)
das_tool 550.0 17.0(0/2) (0/2) (2/2)
diamond 49711.0 963.0(3/3) (3/3) (3/3)
disco 369.0 42.0(1/1) (0/1) (1/1)
dram (0/5) (0/5) (5/5)
drep (0/2) (0/2) (2/2)
export2graphlan 5265.0 200.0(1/1) (1/1) (1/1)
fargene 459.0 52.0(1/1) (0/1) (1/1)
fastp 1055760.0 2803.0(1/1) (1/1) (1/1)
fastqe 4333.0 1266.0(1/1) (1/1) (1/1)
fasttree 55434.0 379.0(1/1) (1/1) (1/1)
filtlong 30483.0 617.0(1/1) (1/1) (1/1)
fraggenescan 1102.0 68.0(0/1) (1/1) (1/1)
freyja (2/4) (0/4) (4/4)
funannotate (3/5) (5/5) (5/5)
glimmer (0/8) (0/8) (4/8)
goenrichment 5206.0 321.0(2/2) (2/2) (2/2)
goseq 19167.0 1210.0(1/1) (1/1) (1/1)
graphlan 5002.0 247.0(2/2) (2/2) (2/2)
gtdbtk (0/1) (1/1) (0/1)
gubbins 3340.0 145.0(1/1) (1/1) (1/1)
hamronization (0/2) (0/2) (2/2)
hansel (1/1) (0/1) (1/1)
hifiasm_meta 137.0 12.0(0/1) (1/1) (1/1)
hmmer3 21049.0 111.0(0/12) (12/12) (12/12)
humann 5856.0 247.0(6/13) (12/13) (13/13)
hyphy (17/17) (2/17) (17/17)
hypo 354.0 39.0(0/1) (0/1) (1/1)
icescreen (0/1) (0/1) (0/1)
idba_ud 721.0 43.0(3/3) (0/3) (3/3)
instrain (0/2) (0/2) (2/2)
interproscan 5294.0 554.0(1/1) (1/1) (1/1)
iqtree 21598.0 681.0(1/1) (1/1) (1/1)
ivar (5/5) (5/5) (5/5)
jbrowse 18229.0 2346.0(2/2) (2/2) (2/2)
jellyfish 1138.0 91.0(0/1) (1/1) (1/1)
kc-align (1/1) (0/1) (1/1)
khmer (8/8) (8/8) (8/8)
kleborate 319.0 38.0(0/1) (0/1) (1/1)
kofamscan 594.0 33.0(0/1) (0/1) (1/1)
kraken_biom 1444.0 182.0(0/1) (1/1) (1/1)
kraken_taxonomy_report 2527.0 354.0(1/1) (1/1) (1/1)
krakentools (1/6) (6/6) (6/6)
krocus (0/1) (0/1) (0/1)
legsta 55.0 7.0(0/1) (0/1) (1/1)
lineagespot 37.0 2.0(0/1) (0/1) (1/1)
lorikeet (0/1) (0/1) (1/1)
m6anet 3.0 (0/1) (0/1) (1/1)
maaslin2 188.0 29.0(0/1) (0/1) (1/1)
maker 4950.0 419.0(2/2) (2/2) (2/2)
mapseq 167.0 2.0(0/1) (0/1) (1/1)
mash 1739.0 12.0(2/2) (2/2) (2/2)
mashmap (0/1) (0/1) (1/1)
maxbin2 2059.0 118.0(1/1) (1/1) (1/1)
mcl 29.0 10.0(0/1) (0/1) (1/1)
medaka (3/4) (3/4) (3/4)
megahit 9530.0 548.0(1/1) (1/1) (1/1)
megahit_contig2fastg 475.0 54.0(1/1) (0/1) (1/1)
megan (0/7) (0/7) (7/7)
meningotype (0/1) (0/1) (0/1)
merqury 2483.0 244.0(2/2) (2/2) (2/2)
meryl 6785.0 350.0(1/1) (1/1) (1/1)
metabat2 4072.0 154.0(2/2) (1/2) (2/2)
metaeuk (0/1) (0/1) (1/1)
metagenomeseq (1/1) (0/1) (1/1)
metaphlan 10507.0 427.0(1/4) (2/4) (4/4)
minia 2206.0 109.0(0/1) (1/1) (1/1)
miniasm 11938.0 178.0(1/1) (1/1) (1/1)
miniprot 813.0 15.0(0/2) (0/2) (2/2)
mitos 32022.0 58.0(1/2) (1/2) (2/2)
mlst 9304.0 635.0(2/2) (2/2) (2/2)
mothur (129/129) (129/129) (129/129)
multigsea 53.0 2.0(0/1) (0/1) (1/1)
multiqc 162790.0 8320.0(1/1) (1/1) (1/1)
mykrobe (0/1) (0/1) (0/1)
nanocompore (0/2) (1/2) (2/2)
nanoplot 63235.0 2195.0(1/1) (1/1) (1/1)
nanopolishcomp (0/2) (0/2) (2/2)
ncbi_fcs_gx (1/1) (0/1) (0/1)
newick_utils 25505.0 448.0(1/1) (1/1) (1/1)
nextclade 3527.0 169.0(1/2) (1/2) (2/2)
nonpareil 142.0 5.0(1/1) (0/1) (1/1)
nugen_nudup (0/1) (0/1) (0/1)
omark (0/1) (0/1) (1/1)
orfipy 774.0 53.0(1/1) (0/1) (1/1)
orthofinder (0/1) (1/1) (1/1)
pharokka 2565.0 74.0(0/1) (1/1) (1/1)
phyloseq (0/3) (0/3) (3/3)
phyml 1770.0 104.0(0/1) (1/1) (1/1)
picrust (0/6) (6/6) (5/6)
picrust2 (0/7) (7/7) (7/7)
plasflow 22589.0 278.0(1/1) (1/1) (1/1)
plasmidfinder 22.0 8.0(0/1) (0/1) (1/1)
prokka 371445.0 3233.0(1/1) (1/1) (1/1)
proteinortho 2092.0 125.0(0/3) (0/3) (3/3)
pycoqc 21123.0 350.0(1/1) (1/1) (1/1)
pygenometracks 11332.0 377.0(1/1) (1/1) (1/1)
qiime_add_on (0/2) (0/2) (2/2)
qiime_core (0/32) (0/32) (32/32)
qualimap (4/4) (4/4) (4/4)
quast 51567.0 3567.0(1/1) (1/1) (1/1)
quickmerge (0/1) (0/1) (0/1)
rasusa (0/1) (0/1) (1/1)
raxml 6808.0 383.0(1/1) (1/1) (1/1)
read_it_and_keep 3370.0 71.0(1/1) (0/1) (1/1)
recentrifuge 331.0 48.0(0/1) (0/1) (1/1)
roary 12225.0 656.0(1/1) (1/1) (1/1)
rseqc 135036.0 3269.0(22/22) (22/22) (22/22)
sarscov2formatter 173.0 7.0(1/1) (0/1) (1/1)
sarscov2summary 140.0 1.0(1/1) (0/1) (1/1)
scoary 676.0 61.0(0/1) (0/1) (1/1)
semibin 183.0 10.0(0/6) (0/6) (6/6)
seqkit (0/3) (0/3) (3/3)
seqprep (0/1) (0/1) (1/1)
seqsero2 12.0 (0/1) (0/1) (1/1)
shovill 41600.0 1008.0(1/1) (1/1) (1/1)
smallgenomeutilities (0/1) (0/1) (1/1)
snap (1/2) (1/2) (1/2)
snippy 105708.0 1372.0(3/3) (3/3) (3/3)
sonneityping 1.0 1.0(0/1) (0/1) (1/1)
spades 58834.0 2309.0(9/9) (9/9) (9/9)
spotyping 1278.0 12.0(0/1) (0/1) (1/1)
srst2 205.0 22.0(0/1) (0/1) (1/1)
structure 2623.0 59.0(0/1) (0/1) (1/1)
taxonomy_krona_chart 27426.0 1801.0(1/1) (1/1) (1/1)
tb-profiler (1/1) (1/1) (1/1)
transtermhp 229.0 5.0(1/1) (0/1) (1/1)
unicycler 65732.0 1558.0(1/1) (1/1) (1/1)
usher 1060.0 5.0(0/2) (0/2) (2/2)
valet 637.0 20.0(1/1) (0/1) (1/1)
vapor 3164.0 94.0(1/1) (0/1) (1/1)
varvamp (0/1) (0/1) (1/1)
vegan (3/3) (0/3) (3/3)
velvet 12218.0 1280.0(2/2) (2/2) (2/2)
velvet_optimiser (1/1) (1/1) (1/1)
vsearch 8507.0 182.0(8/8) (8/8) (8/8)
windowmasker 85.0 (0/2) (2/2) (2/2)
bamtools 14039.0 208.0(1/1) (0/1) (1/1)
biotradis (3/3) (0/3) (0/3)
kraken 13938.0 404.0(5/5) (5/5) (5/5)
kraken2 185308.0 2367.0(1/1) (1/1) (1/1)
eggnog_mapper 30565.0 510.0(1/3) (3/3) (3/3)
metagene_annotator 636.0 115.0(0/1) (0/1) (1/1)
ez_histograms (0/1) (0/1) (0/1)
Geom_mean_workflow (0/3) (0/3) (3/3)
PAMPA (0/5) (5/5) (5/5)
interpolation (0/1) (0/1) (1/1)
medenv (0/1) (0/1) (1/1)
obisindicators 45.0 4.0(1/2) (0/2) (2/2)
ocean (0/1) (0/1) (1/1)
blast2go 1232.0 101.0(0/1) (0/1) (0/1)
blast_rbh 22499.0 121.0(0/1) (0/1) (1/1)
blastxml_to_top_descr 264558.0 159.0(0/1) (0/1) (1/1)
make_nr (0/1) (0/1) (0/1)
ncbi_blast_plus 365597.0 4066.0(16/18) (16/18) (16/18)