@galaxyproject/igv 0.0.4 → 0.0.6
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/package.json +2 -2
- package/static/igv.xml +39 -54
- package/static/index.css +1 -1
- package/static/index.js +237 -237
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@galaxyproject/igv",
|
|
3
|
-
"version": "0.0.
|
|
3
|
+
"version": "0.0.6",
|
|
4
4
|
"type": "module",
|
|
5
5
|
"license": "MIT",
|
|
6
6
|
"files": [
|
|
@@ -20,7 +20,7 @@
|
|
|
20
20
|
"@vitejs/plugin-vue": "^5.0.5",
|
|
21
21
|
"@vitest/ui": "^3.0.9",
|
|
22
22
|
"autoprefixer": "^10.4.19",
|
|
23
|
-
"galaxy-charts": "^0.0.
|
|
23
|
+
"galaxy-charts": "^0.0.80",
|
|
24
24
|
"galaxy-charts-xml-parser": "^1.0.3",
|
|
25
25
|
"igv": "^3.5.0",
|
|
26
26
|
"jsdom": "^25.0.1",
|
package/static/igv.xml
CHANGED
|
@@ -5,22 +5,18 @@
|
|
|
5
5
|
<data_sources>
|
|
6
6
|
<data_source>
|
|
7
7
|
<model_class>HistoryDatasetAssociation</model_class>
|
|
8
|
-
<test test_attr="ext">2bit</test>
|
|
9
8
|
<test test_attr="ext">bam</test>
|
|
10
9
|
<test test_attr="ext">bcf</test>
|
|
11
10
|
<test test_attr="ext">bed</test>
|
|
12
11
|
<test test_attr="ext">bedgraph</test>
|
|
13
12
|
<test test_attr="ext">bigbed</test>
|
|
14
13
|
<test test_attr="ext">bigwig</test>
|
|
15
|
-
<test test_attr="ext">broadpeak</test>
|
|
16
|
-
<test test_attr="ext">bw</test>
|
|
17
14
|
<test test_attr="ext">cram</test>
|
|
18
|
-
<test test_attr="ext">fa</test>
|
|
19
15
|
<test test_attr="ext">fasta</test>
|
|
20
16
|
<test test_attr="ext">gff</test>
|
|
21
17
|
<test test_attr="ext">gff3</test>
|
|
22
18
|
<test test_attr="ext">gtf</test>
|
|
23
|
-
<test test_attr="ext">
|
|
19
|
+
<test test_attr="ext">twobit</test>
|
|
24
20
|
<test test_attr="ext">vcf</test>
|
|
25
21
|
<test test_attr="ext">vcf_bgzip</test>
|
|
26
22
|
<test test_attr="ext">wig</test>
|
|
@@ -32,55 +28,44 @@
|
|
|
32
28
|
<entry_point entry_point_type="script" src="index.js" css="index.css" />
|
|
33
29
|
<settings>
|
|
34
30
|
<input>
|
|
35
|
-
<label>
|
|
36
|
-
<help>
|
|
37
|
-
<name>
|
|
38
|
-
<type>
|
|
39
|
-
<
|
|
40
|
-
|
|
41
|
-
|
|
42
|
-
<
|
|
43
|
-
|
|
44
|
-
|
|
45
|
-
<
|
|
46
|
-
|
|
47
|
-
|
|
48
|
-
|
|
49
|
-
|
|
50
|
-
|
|
51
|
-
|
|
52
|
-
|
|
53
|
-
|
|
54
|
-
|
|
55
|
-
|
|
56
|
-
|
|
57
|
-
|
|
58
|
-
|
|
59
|
-
|
|
60
|
-
<
|
|
61
|
-
|
|
62
|
-
|
|
63
|
-
|
|
64
|
-
|
|
65
|
-
|
|
66
|
-
|
|
67
|
-
|
|
68
|
-
|
|
69
|
-
|
|
70
|
-
|
|
71
|
-
|
|
72
|
-
|
|
73
|
-
<data><label>D. melanogaster (dm3)</label><value>dm3</value></data>
|
|
74
|
-
<data><label>D. melanogaster (dmel_r5.9)</label><value>dmel_r5.9</value></data>
|
|
75
|
-
<data><label>S. cerevisiae (sacCer3)</label><value>sacCer3</value></data>
|
|
76
|
-
<data><label>S. pombe (ASM294v2)</label><value>ASM294v2</value></data>
|
|
77
|
-
<data><label>Sars-CoV-2 (ASM985889v3)</label><value>ASM985889v3</value></data>
|
|
78
|
-
<data><label>A. thaliana (TAIR 10)</label><value>tair10</value></data>
|
|
79
|
-
<data><label>Peanut (GCA_003086295.2)</label><value>GCA_003086295.2</value></data>
|
|
80
|
-
<data><label>O. sativa IRGSP-1.0 (GCF_001433935.1)</label><value>GCF_001433935.1</value></data>
|
|
81
|
-
<data><label>Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S</label><value>NC_016856.1</value></data>
|
|
82
|
-
<data><label>Coprinopsis cinerea okayama7#130 (GCA_000182895.1)</label><value>GCA_000182895.1</value></data>
|
|
83
|
-
</data>
|
|
31
|
+
<label>Source</label>
|
|
32
|
+
<help>Switch to genomes provided IGV</help>
|
|
33
|
+
<name>source</name>
|
|
34
|
+
<type>conditional</type>
|
|
35
|
+
<test_param>
|
|
36
|
+
<name>from_igv</name>
|
|
37
|
+
<type>boolean</type>
|
|
38
|
+
<value>false</value>
|
|
39
|
+
</test_param>
|
|
40
|
+
<cases>
|
|
41
|
+
<cases>
|
|
42
|
+
<value>false</value>
|
|
43
|
+
<inputs>
|
|
44
|
+
<inputs>
|
|
45
|
+
<label>Genome</label>
|
|
46
|
+
<help>Select a reference genome</help>
|
|
47
|
+
<name>genome</name>
|
|
48
|
+
<type>data_table</type>
|
|
49
|
+
<tables>
|
|
50
|
+
<tables>fasta_indexes</tables>
|
|
51
|
+
<tables>twobit</tables>
|
|
52
|
+
</tables>
|
|
53
|
+
</inputs>
|
|
54
|
+
</inputs>
|
|
55
|
+
</cases>
|
|
56
|
+
<cases>
|
|
57
|
+
<value>true</value>
|
|
58
|
+
<inputs>
|
|
59
|
+
<inputs>
|
|
60
|
+
<label>Genome</label>
|
|
61
|
+
<help>Select a reference genome provided by IGV</help>
|
|
62
|
+
<name>genome</name>
|
|
63
|
+
<type>data_json</type>
|
|
64
|
+
<url>https://s3.amazonaws.com/igv.org.genomes/genomes.json</url>
|
|
65
|
+
</inputs>
|
|
66
|
+
</inputs>
|
|
67
|
+
</cases>
|
|
68
|
+
</cases>
|
|
84
69
|
</input>
|
|
85
70
|
<input>
|
|
86
71
|
<label>Locus</label>
|
package/static/index.css
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
html,:host{line-height:1.5;-webkit-text-size-adjust:100%;-moz-tab-size:4;-o-tab-size:4;tab-size:4;font-family:ui-sans-serif,system-ui,sans-serif,"Apple Color Emoji","Segoe UI Emoji",Segoe UI Symbol,"Noto Color Emoji";font-feature-settings:normal;font-variation-settings:normal;-webkit-tap-highlight-color:transparent}code,kbd,samp,pre{font-family:ui-monospace,SFMono-Regular,Menlo,Monaco,Consolas,Liberation Mono,Courier New,monospace;font-feature-settings:normal;font-variation-settings:normal;font-size:1em}.visible{visibility:visible}.absolute{position:absolute}.relative{position:relative}.right-0{right:0}.z-10{z-index:10}.z-\[1\]{z-index:1}.m-2{margin:.5rem}.mx-1{margin-left:.25rem;margin-right:.25rem}.mx-2{margin-left:.5rem;margin-right:.5rem}.my-1{margin-top:.25rem;margin-bottom:.25rem}.my-2{margin-top:.5rem;margin-bottom:.5rem}.mb-1{margin-bottom:.25rem}.mb-2{margin-bottom:.5rem}.mr-1{margin-right:.25rem}.mr-2{margin-right:.5rem}.mt-
|
|
1
|
+
html,:host{line-height:1.5;-webkit-text-size-adjust:100%;-moz-tab-size:4;-o-tab-size:4;tab-size:4;font-family:ui-sans-serif,system-ui,sans-serif,"Apple Color Emoji","Segoe UI Emoji",Segoe UI Symbol,"Noto Color Emoji";font-feature-settings:normal;font-variation-settings:normal;-webkit-tap-highlight-color:transparent}code,kbd,samp,pre{font-family:ui-monospace,SFMono-Regular,Menlo,Monaco,Consolas,Liberation Mono,Courier New,monospace;font-feature-settings:normal;font-variation-settings:normal;font-size:1em}.visible{visibility:visible}.absolute{position:absolute}.relative{position:relative}.right-0{right:0}.z-10{z-index:10}.z-\[1\]{z-index:1}.m-2{margin:.5rem}.mx-1{margin-left:.25rem;margin-right:.25rem}.mx-2{margin-left:.5rem;margin-right:.5rem}.my-1{margin-top:.25rem;margin-bottom:.25rem}.my-2{margin-top:.5rem;margin-bottom:.5rem}.mb-1{margin-bottom:.25rem}.mb-2{margin-bottom:.5rem}.mr-1{margin-right:.25rem}.mr-2{margin-right:.5rem}.mt-2{margin-top:.5rem}.block{display:block}.inline{display:inline}.flex{display:flex}.grid{display:grid}.contents{display:contents}.\!hidden{display:none!important}.hidden{display:none}.size-14{width:3.5rem;height:3.5rem}.size-3{width:.75rem;height:.75rem}.size-4{width:1rem;height:1rem}.w-full{width:100%}.w-screen{width:100vw}.min-w-14{min-width:3.5rem}.max-w-14{max-width:3.5rem}.max-w-full{max-width:100%}.flex-1{flex:1 1 0%}@keyframes spin{to{transform:rotate(360deg)}}.animate-spin{animation:spin 1s linear infinite}.select-none{-webkit-user-select:none;-moz-user-select:none;user-select:none}.resize{resize:both}.grid-cols-\[1fr_17rem\]{grid-template-columns:1fr 17rem}.justify-center{justify-content:center}.overflow-hidden{overflow:hidden}.\!overflow-visible{overflow:visible!important}.text-ellipsis{text-overflow:ellipsis}.whitespace-normal{white-space:normal}.whitespace-nowrap{white-space:nowrap}.whitespace-pre{white-space:pre}.break-words{overflow-wrap:break-word}.break-all{word-break:break-all}.border-dotted{border-style:dotted}.border-green-600{--tw-border-opacity: 1;border-color:rgb(22 163 74 / var(--tw-border-opacity))}.bg-gray-600{--tw-bg-opacity: 1;background-color:rgb(75 85 99 / var(--tw-bg-opacity))}.bg-sky-50{--tw-bg-opacity: 1;background-color:rgb(240 249 255 / var(--tw-bg-opacity))}.bg-white{--tw-bg-opacity: 1;background-color:rgb(255 255 255 / var(--tw-bg-opacity))}.object-contain{-o-object-fit:contain;object-fit:contain}.p-1{padding:.25rem}.p-4{padding:1rem}.py-1{padding-top:.25rem;padding-bottom:.25rem}.py-2{padding-top:.5rem;padding-bottom:.5rem}.pb-2{padding-bottom:.5rem}.text-lg{font-size:1.125rem;line-height:1.75rem}.text-xs{font-size:.75rem;line-height:1rem}.font-bold{font-weight:700}.font-thin{font-weight:100}.text-green-600{--tw-text-opacity: 1;color:rgb(22 163 74 / var(--tw-text-opacity))}.text-red-600{--tw-text-opacity: 1;color:rgb(220 38 38 / var(--tw-text-opacity))}.text-sky-900{--tw-text-opacity: 1;color:rgb(12 74 110 / var(--tw-text-opacity))}.text-white{--tw-text-opacity: 1;color:rgb(255 255 255 / var(--tw-text-opacity))}*,:before,:after{box-sizing:border-box;border-width:0;border-style:solid;border-color:#e5e7eb}:before,:after{--tw-content: ""}html,:host{line-height:1.5;-webkit-text-size-adjust:100%;-moz-tab-size:4;-o-tab-size:4;tab-size:4;font-family:ui-sans-serif,system-ui,sans-serif,"Apple Color Emoji","Segoe UI Emoji",Segoe UI Symbol,"Noto Color Emoji";font-feature-settings:normal;font-variation-settings:normal;-webkit-tap-highlight-color:transparent}body{margin:0;line-height:inherit}hr{height:0;color:inherit;border-top-width:1px}abbr:where([title]){-webkit-text-decoration:underline dotted;text-decoration:underline dotted}h1,h2,h3,h4,h5,h6{font-size:inherit;font-weight:inherit}a{color:inherit;text-decoration:inherit}b,strong{font-weight:bolder}code,kbd,samp,pre{font-family:ui-monospace,SFMono-Regular,Menlo,Monaco,Consolas,Liberation Mono,Courier New,monospace;font-feature-settings:normal;font-variation-settings:normal;font-size:1em}small{font-size:80%}sub,sup{font-size:75%;line-height:0;position:relative;vertical-align:baseline}sub{bottom:-.25em}sup{top:-.5em}table{text-indent:0;border-color:inherit;border-collapse:collapse}button,input,optgroup,select,textarea{font-family:inherit;font-feature-settings:inherit;font-variation-settings:inherit;font-size:100%;font-weight:inherit;line-height:inherit;letter-spacing:inherit;color:inherit;margin:0;padding:0}button,select{text-transform:none}button,input:where([type=button]),input:where([type=reset]),input:where([type=submit]){-webkit-appearance:button;background-color:transparent;background-image:none}:-moz-focusring{outline:auto}:-moz-ui-invalid{box-shadow:none}progress{vertical-align:baseline}::-webkit-inner-spin-button,::-webkit-outer-spin-button{height:auto}[type=search]{-webkit-appearance:textfield;outline-offset:-2px}::-webkit-search-decoration{-webkit-appearance:none}::-webkit-file-upload-button{-webkit-appearance:button;font:inherit}summary{display:list-item}blockquote,dl,dd,h1,h2,h3,h4,h5,h6,hr,figure,p,pre{margin:0}fieldset{margin:0;padding:0}legend{padding:0}ol,ul,menu{list-style:none;margin:0;padding:0}dialog{padding:0}textarea{resize:vertical}input::-moz-placeholder,textarea::-moz-placeholder{opacity:1;color:#9ca3af}input::placeholder,textarea::placeholder{opacity:1;color:#9ca3af}button,[role=button]{cursor:pointer}:disabled{cursor:default}img,svg,video,canvas,audio,iframe,embed,object{display:block;vertical-align:middle}img,video{max-width:100%;height:auto}[hidden]{display:none}*,:before,:after{--tw-border-spacing-x: 0;--tw-border-spacing-y: 0;--tw-translate-x: 0;--tw-translate-y: 0;--tw-rotate: 0;--tw-skew-x: 0;--tw-skew-y: 0;--tw-scale-x: 1;--tw-scale-y: 1;--tw-pan-x: ;--tw-pan-y: ;--tw-pinch-zoom: ;--tw-scroll-snap-strictness: proximity;--tw-gradient-from-position: ;--tw-gradient-via-position: ;--tw-gradient-to-position: ;--tw-ordinal: ;--tw-slashed-zero: ;--tw-numeric-figure: ;--tw-numeric-spacing: ;--tw-numeric-fraction: ;--tw-ring-inset: ;--tw-ring-offset-width: 0px;--tw-ring-offset-color: #fff;--tw-ring-color: rgb(59 130 246 / .5);--tw-ring-offset-shadow: 0 0 #0000;--tw-ring-shadow: 0 0 #0000;--tw-shadow: 0 0 #0000;--tw-shadow-colored: 0 0 #0000;--tw-blur: ;--tw-brightness: ;--tw-contrast: ;--tw-grayscale: ;--tw-hue-rotate: ;--tw-invert: ;--tw-saturate: ;--tw-sepia: ;--tw-drop-shadow: ;--tw-backdrop-blur: ;--tw-backdrop-brightness: ;--tw-backdrop-contrast: ;--tw-backdrop-grayscale: ;--tw-backdrop-hue-rotate: ;--tw-backdrop-invert: ;--tw-backdrop-opacity: ;--tw-backdrop-saturate: ;--tw-backdrop-sepia: ;--tw-contain-size: ;--tw-contain-layout: ;--tw-contain-paint: ;--tw-contain-style: }::backdrop{--tw-border-spacing-x: 0;--tw-border-spacing-y: 0;--tw-translate-x: 0;--tw-translate-y: 0;--tw-rotate: 0;--tw-skew-x: 0;--tw-skew-y: 0;--tw-scale-x: 1;--tw-scale-y: 1;--tw-pan-x: ;--tw-pan-y: ;--tw-pinch-zoom: ;--tw-scroll-snap-strictness: proximity;--tw-gradient-from-position: ;--tw-gradient-via-position: ;--tw-gradient-to-position: ;--tw-ordinal: ;--tw-slashed-zero: ;--tw-numeric-figure: ;--tw-numeric-spacing: ;--tw-numeric-fraction: ;--tw-ring-inset: ;--tw-ring-offset-width: 0px;--tw-ring-offset-color: #fff;--tw-ring-color: rgb(59 130 246 / .5);--tw-ring-offset-shadow: 0 0 #0000;--tw-ring-shadow: 0 0 #0000;--tw-shadow: 0 0 #0000;--tw-shadow-colored: 0 0 #0000;--tw-blur: ;--tw-brightness: ;--tw-contrast: ;--tw-grayscale: ;--tw-hue-rotate: ;--tw-invert: ;--tw-saturate: ;--tw-sepia: ;--tw-drop-shadow: ;--tw-backdrop-blur: ;--tw-backdrop-brightness: ;--tw-backdrop-contrast: ;--tw-backdrop-grayscale: ;--tw-backdrop-hue-rotate: ;--tw-backdrop-invert: ;--tw-backdrop-opacity: ;--tw-backdrop-saturate: ;--tw-backdrop-sepia: ;--tw-contain-size: ;--tw-contain-layout: ;--tw-contain-paint: ;--tw-contain-style: }.container{width:100%}@media (min-width: 640px){.container{max-width:640px}}@media (min-width: 768px){.container{max-width:768px}}@media (min-width: 1024px){.container{max-width:1024px}}@media (min-width: 1280px){.container{max-width:1280px}}@media (min-width: 1536px){.container{max-width:1536px}}.mt-1{margin-top:.25rem}.table{display:table}.h-screen{height:100vh}.overflow-auto{overflow:auto}.rounded{border-radius:.25rem}.border{border-width:1px}.border-sky-200{--tw-border-opacity: 1;border-color:rgb(186 230 253 / var(--tw-border-opacity))}.bg-sky-100{--tw-bg-opacity: 1;background-color:rgb(224 242 254 / var(--tw-bg-opacity))}.p-2{padding:.5rem}.text-sm{font-size:.875rem;line-height:1.25rem}.text-sky-800{--tw-text-opacity: 1;color:rgb(7 89 133 / var(--tw-text-opacity))}.filter{filter:var(--tw-blur) var(--tw-brightness) var(--tw-contrast) var(--tw-grayscale) var(--tw-hue-rotate) var(--tw-invert) var(--tw-saturate) var(--tw-sepia) var(--tw-drop-shadow)}
|