view x/static/js/2989.031b43a0.chunk.js @ 125:49f3d3878413 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566
author fubar
date Sat, 05 Oct 2024 23:58:05 +0000
parents
children
line wrap: on
line source

"use strict";(globalThis.webpackChunk_jbrowse_web=globalThis.webpackChunk_jbrowse_web||[]).push([[2989],{12989:(e,t,a)=>{a.r(t),a.d(t,{default:()=>y});var n=a(7552),r=a(68446),l=a(1343),o=a(29499),i=a(36715),s=a(87731),c=a(943),u=a(58507),p=a(5401),d=a(49823);const m=(0,a(75785).n9)()((e=>({paper:{padding:e.spacing(2),margin:e.spacing(2)},field:{margin:e.spacing(2)}}))),g=["read paired","read mapped in proper pair","read unmapped","mate unmapped","read reverse strand","mate reverse strand","first in pair","second in pair","not primary alignment","read fails platform/vendor quality checks","read is PCR or optical duplicate","supplementary alignment"];function v(e){const{flag:t=0,setFlag:a}=e;return n.createElement(n.Fragment,null,n.createElement(l.A,{type:"number",value:t,onChange:e=>{a(+e.target.value)}}),g.map(((e,r)=>{const l=t&1<<r,o=`${e}_${l}`;return n.createElement("div",{key:o},n.createElement("input",{type:"checkbox",checked:Boolean(l),onChange:e=>{e.target.checked?a(t|1<<r):a(t&~(1<<r))}}),n.createElement("label",{htmlFor:o},e))})))}const y=(0,r.observer)((function(e){const{model:t,handleClose:a}=e,{classes:r}=m(),{filterBy:g}=t,[y,h]=(0,n.useState)(g.flagInclude),[b,f]=(0,n.useState)(g.flagExclude),[A,E]=(0,n.useState)(g.tagFilter?.tag||""),[x,C]=(0,n.useState)(g.tagFilter?.value||""),[k,w]=(0,n.useState)(g.readName||""),S=/^[A-Za-z][A-Za-z0-9]$/.exec(A),F="https://broadinstitute.github.io/picard/explain-flags.html";return n.createElement(d.Dialog,{open:!0,onClose:a,title:"Filter options"},n.createElement(o.A,null,n.createElement(i.A,null,"Set filter bitmask options. Refer to ",n.createElement(s.A,{href:F},F)," ","for details"),n.createElement(c.A,{className:r.paper,variant:"outlined"},n.createElement("div",{style:{display:"flex"}},n.createElement("div",null,n.createElement(i.A,null,"Read must have ALL these flags"),n.createElement(v,{flag:y,setFlag:h})),n.createElement("div",null,n.createElement(i.A,null,"Read must have NONE of these flags"),n.createElement(v,{flag:b,setFlag:f})))),n.createElement(c.A,{className:r.paper,variant:"outlined"},n.createElement(i.A,null,"Filter by tag name and value. Use * in the value field to get all reads containing any value for that tag. Example: filter tag name SA with value * to get all split/supplementary reads. Other examples include HP for haplotype, or RG for read group"),n.createElement(l.A,{className:r.field,value:A,onChange:e=>{E(e.target.value)},placeholder:"Enter tag name",inputProps:{maxLength:2},error:2===A.length&&!S,helperText:2!==A.length||S?"":"Not a valid tag"}),n.createElement(l.A,{className:r.field,value:x,onChange:e=>{C(e.target.value)},placeholder:"Enter tag value"})),n.createElement(c.A,{className:r.paper,variant:"outlined"},n.createElement(i.A,null,"Filter by read name"),n.createElement(l.A,{className:r.field,value:k,onChange:e=>{w(e.target.value)},placeholder:"Enter read name"})),n.createElement(u.A,null,n.createElement(p.A,{variant:"contained",color:"primary",autoFocus:!0,type:"submit",onClick:()=>{t.setFilterBy({flagInclude:y,flagExclude:b,readName:k,tagFilter:""!==A?{tag:A,value:x}:void 0}),a()}},"Submit"),n.createElement(p.A,{variant:"contained",color:"secondary",onClick:()=>{a()}},"Cancel"))))}))},87731:(e,t,a)=>{a.d(t,{A:()=>E});var n=a(7552),r=a(93878),l=a(72639),o=a(70799),i=a(91527),s=a(15622),c=a(51148),u=a(48231),p=a(60129),d=a(58520),m=a(4785),g=a(36715),v=a(58161),y=a(39995);const h=({theme:e,ownerState:t})=>{const a=t.color,n=(0,y.Yn)(e,`palette.${a}`,!1)||t.color,r=(0,y.Yn)(e,`palette.${a}Channel`);return"vars"in e&&r?`rgba(${r} / 0.4)`:(0,l.X4)(n,.4)};var b=a(69500);const f={primary:!0,secondary:!0,error:!0,info:!0,success:!0,warning:!0,textPrimary:!0,textSecondary:!0,textDisabled:!0},A=(0,c.Ay)(g.A,{name:"MuiLink",slot:"Root",overridesResolver:(e,t)=>{const{ownerState:a}=e;return[t.root,t[`underline${(0,s.A)(a.underline)}`],"button"===a.component&&t.button]}})((0,p.A)((({theme:e})=>({variants:[{props:{underline:"none"},style:{textDecoration:"none"}},{props:{underline:"hover"},style:{textDecoration:"none","&:hover":{textDecoration:"underline"}}},{props:{underline:"always"},style:{textDecoration:"underline","&:hover":{textDecorationColor:"inherit"}}},{props:({underline:e,ownerState:t})=>"always"===e&&"inherit"!==t.color,style:{textDecorationColor:"var(--Link-underlineColor)"}},...Object.entries(e.palette).filter((0,d.A)()).map((([t])=>({props:{underline:"always",color:t},style:{"--Link-underlineColor":e.vars?`rgba(${e.vars.palette[t].mainChannel} / 0.4)`:(0,l.X4)(e.palette[t].main,.4)}}))),{props:{underline:"always",color:"textPrimary"},style:{"--Link-underlineColor":e.vars?`rgba(${e.vars.palette.text.primaryChannel} / 0.4)`:(0,l.X4)(e.palette.text.primary,.4)}},{props:{underline:"always",color:"textSecondary"},style:{"--Link-underlineColor":e.vars?`rgba(${e.vars.palette.text.secondaryChannel} / 0.4)`:(0,l.X4)(e.palette.text.secondary,.4)}},{props:{underline:"always",color:"textDisabled"},style:{"--Link-underlineColor":(e.vars||e).palette.text.disabled}},{props:{component:"button"},style:{position:"relative",WebkitTapHighlightColor:"transparent",backgroundColor:"transparent",outline:0,border:0,margin:0,borderRadius:0,padding:0,cursor:"pointer",userSelect:"none",verticalAlign:"middle",MozAppearance:"none",WebkitAppearance:"none","&::-moz-focus-inner":{borderStyle:"none"},[`&.${v.A.focusVisible}`]:{outline:"auto"}}}]})))),E=n.forwardRef((function(e,t){const a=(0,m.b)({props:e,name:"MuiLink"}),l=(0,u.A)(),{className:c,color:p="primary",component:d="a",onBlur:g,onFocus:y,TypographyClasses:E,underline:x="always",variant:C="inherit",sx:k,...w}=a,[S,F]=n.useState(!1),N={...a,color:p,component:d,focusVisible:S,underline:x,variant:C},L=(e=>{const{classes:t,component:a,focusVisible:n,underline:r}=e,l={root:["root",`underline${(0,s.A)(r)}`,"button"===a&&"button",n&&"focusVisible"]};return(0,o.A)(l,v.t,t)})(N);return(0,b.jsx)(A,{color:p,className:(0,r.A)(L.root,c),classes:E,component:d,onBlur:e=>{(0,i.A)(e.target)||F(!1),g&&g(e)},onFocus:e=>{(0,i.A)(e.target)&&F(!0),y&&y(e)},ref:t,ownerState:N,variant:C,...w,sx:[...void 0===f[p]?[{color:p}]:[],...Array.isArray(k)?k:[k]],style:{...w.style,..."always"===x&&"inherit"!==p&&!f[p]&&{"--Link-underlineColor":h({theme:l,ownerState:N})}}})}))},58161:(e,t,a)=>{a.d(t,{A:()=>o,t:()=>l});var n=a(33761),r=a(85693);function l(e){return(0,r.Ay)("MuiLink",e)}const o=(0,n.A)("MuiLink",["root","underlineNone","underlineHover","underlineAlways","button","focusVisible"])}}]);
//# sourceMappingURL=2989.031b43a0.chunk.js.map