Mercurial > repos > cpt > cpt_xmfa
changeset 1:bfe0d989004d draft
planemo upload commit 94b0cd1fff0826c6db3e7dc0c91c0c5a8be8bb0c
| author | cpt |
|---|---|
| date | Mon, 05 Jun 2023 02:54:26 +0000 |
| parents | b4d7351df1ff |
| children | 67bd43a712fb |
| files | cpt-macros.xml cpt_xmfa/cpt-macros.xml cpt_xmfa/macros.xml cpt_xmfa/mauve.js cpt_xmfa/mauve.xml cpt_xmfa/xmfa_process.py macros.xml mauve.js mauve.xml xmfa_process.py |
| diffstat | 10 files changed, 405 insertions(+), 396 deletions(-) [+] |
line wrap: on
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cpt-macros.xml Mon Jun 05 02:54:26 2023 +0000 @@ -0,0 +1,115 @@ +<macros> + <xml name="gff_requirements"> + <requirements> + <requirement type="package" version="2.7">python</requirement> + <requirement type="package" version="1.65">biopython</requirement> + <requirement type="package" version="2.12.1">requests</requirement> + <requirement type="package" version="1.2.2">cpt_gffparser</requirement> + <yield/> + </requirements> + <version_command> + <![CDATA[ + cd '$__tool_directory__' && git rev-parse HEAD + ]]> + </version_command> + </xml> + <xml name="citation/mijalisrasche"> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex">@unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-crr"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {C. Ross}, + title = {CPT Galaxy Tools}, + year = {2020-}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-2020"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {E. Mijalis, H. Rasche}, + title = {CPT Galaxy Tools}, + year = {2013-2017}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {A. Criscione}, + title = {CPT Galaxy Tools}, + year = {2019-2021}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-2020-AJC-solo"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {A. Criscione}, + title = {CPT Galaxy Tools}, + year = {2019-2021}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="citations-clm"> + <citations> + <citation type="doi">10.1371/journal.pcbi.1008214</citation> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {C. Maughmer}, + title = {CPT Galaxy Tools}, + year = {2017-2020}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </citations> + </xml> + <xml name="sl-citations-clm"> + <citation type="bibtex"> + @unpublished{galaxyTools, + author = {C. Maughmer}, + title = {CPT Galaxy Tools}, + year = {2017-2020}, + note = {https://github.com/tamu-cpt/galaxy-tools/} + } + </citation> + <yield/> + </xml> +</macros>
--- a/cpt_xmfa/cpt-macros.xml Tue Jul 05 05:07:32 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,115 +0,0 @@ -<?xml version="1.0"?> -<macros> - <xml name="gff_requirements"> - <requirements> - <requirement type="package" version="2.7">python</requirement> - <requirement type="package" version="1.65">biopython</requirement> - <requirement type="package" version="2.12.1">requests</requirement> - <yield/> - </requirements> - <version_command> - <![CDATA[ - cd $__tool_directory__ && git rev-parse HEAD - ]]> - </version_command> - </xml> - <xml name="citation/mijalisrasche"> - <citation type="doi">10.1371/journal.pcbi.1008214</citation> - <citation type="bibtex">@unpublished{galaxyTools, - author = {E. Mijalis, H. Rasche}, - title = {CPT Galaxy Tools}, - year = {2013-2017}, - note = {https://github.com/tamu-cpt/galaxy-tools/} - } - </citation> - </xml> - <xml name="citations"> - <citations> - <citation type="doi">10.1371/journal.pcbi.1008214</citation> - <citation type="bibtex"> - @unpublished{galaxyTools, - author = {E. Mijalis, H. Rasche}, - title = {CPT Galaxy Tools}, - year = {2013-2017}, - note = {https://github.com/tamu-cpt/galaxy-tools/} - } - </citation> - <yield/> - </citations> - </xml> - <xml name="citations-crr"> - <citations> - <citation type="doi">10.1371/journal.pcbi.1008214</citation> - <citation type="bibtex"> - @unpublished{galaxyTools, - author = {C. Ross}, - title = {CPT Galaxy Tools}, - year = {2020-}, - note = {https://github.com/tamu-cpt/galaxy-tools/} - } - </citation> - <yield/> - </citations> - </xml> - <xml name="citations-2020"> - <citations> - <citation type="doi">10.1371/journal.pcbi.1008214</citation> - <citation type="bibtex"> - @unpublished{galaxyTools, - author = {E. Mijalis, H. Rasche}, - title = {CPT Galaxy Tools}, - year = {2013-2017}, - note = {https://github.com/tamu-cpt/galaxy-tools/} - } - </citation> - <citation type="bibtex"> - @unpublished{galaxyTools, - author = {A. Criscione}, - title = {CPT Galaxy Tools}, - year = {2019-2021}, - note = {https://github.com/tamu-cpt/galaxy-tools/} - } - </citation> - <yield/> - </citations> - </xml> - <xml name="citations-2020-AJC-solo"> - <citations> - <citation type="doi">10.1371/journal.pcbi.1008214</citation> - <citation type="bibtex"> - @unpublished{galaxyTools, - author = {A. Criscione}, - title = {CPT Galaxy Tools}, - year = {2019-2021}, - note = {https://github.com/tamu-cpt/galaxy-tools/} - } - </citation> - <yield/> - </citations> - </xml> - <xml name="citations-clm"> - <citations> - <citation type="doi">10.1371/journal.pcbi.1008214</citation> - <citation type="bibtex"> - @unpublished{galaxyTools, - author = {C. Maughmer}, - title = {CPT Galaxy Tools}, - year = {2017-2020}, - note = {https://github.com/tamu-cpt/galaxy-tools/} - } - </citation> - <yield/> - </citations> - </xml> - <xml name="sl-citations-clm"> - <citation type="bibtex"> - @unpublished{galaxyTools, - author = {C. Maughmer}, - title = {CPT Galaxy Tools}, - year = {2017-2020}, - note = {https://github.com/tamu-cpt/galaxy-tools/} - } - </citation> - <yield/> - </xml> -</macros>
--- a/cpt_xmfa/macros.xml Tue Jul 05 05:07:32 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,61 +0,0 @@ -<?xml version="1.0"?> -<macros> - <xml name="requirements"> - <requirements> - <requirement type="package">progressivemauve</requirement> - <requirement type="package" version="3.8.13">python</requirement> - <requirement type="package" version="1.79">biopython</requirement> - <requirement type="package" version="1.2.2">cpt_gffparser</requirement> - <yield/> - </requirements> - </xml> - <token name="@WRAPPER_VERSION@">2.4.0</token> - <xml name="citation/progressive_mauve"> - <citation type="doi">10.1371/journal.pone.0011147</citation> - </xml> - <xml name="citation/gepard"> - <citation type="doi">10.1093/bioinformatics/btm039</citation> - </xml> - - <token name="@XMFA_INPUT@"> - "$xmfa" - </token> - <xml name="xmfa_input" - token_formats="xmfa"> - <param type="data" format="@FORMATS@" name="xmfa" label="XMFA MSA" /> - </xml> - - <token name="@XMFA_FA_INPUT@"> - "$sequences" - </token> - <xml name="xmfa_fa_input"> - <param type="data" format="fasta" name="sequences" label="Sequences in alignment" - help="These sequences should be the SAME DATASET that was used in the progressiveMauve run. Failing that, they should be provided in the same order as in original progressiveMauve run"/> - - </xml> - <xml name="genome_selector"> - <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/> - </xml> - <xml name="gff3_input"> - <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/> - </xml> - <xml name="input/gff3+fasta"> - <expand macro="gff3_input" /> - <expand macro="genome_selector" /> - </xml> - <token name="@INPUT_GFF@"> - "$gff3_data" - </token> - <token name="@INPUT_FASTA@"> - genomeref.fa - </token> - <token name="@GENOME_SELECTOR_PRE@"> - ln -s $genome_fasta genomeref.fa; - </token> - <token name="@GENOME_SELECTOR@"> - genomeref.fa - </token> - <xml name="input/fasta"> - <param label="Fasta file" name="sequences" type="data" format="fasta"/> - </xml> -</macros>
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n?new wt(t,n):new mt(t,0)}return e.alpha=function(n){return t(+n)},e}(.5);Mt.prototype={areaStart:Qf,areaEnd:Qf,lineStart:function(){this._point=0},lineEnd:function(){this._point&&this._context.closePath()},point:function(t,n){t=+t,n=+n,this._point?this._context.lineTo(t,n):(this._point=1,this._context.moveTo(t,n))}};var ch=function(t){return new Mt(t)};Nt.prototype={areaStart:function(){this._line=0},areaEnd:function(){this._line=NaN},lineStart:function(){this._x0=this._x1=this._y0=this._y1=this._t0=NaN,this._point=0},lineEnd:function(){switch(this._point){case 2:this._context.lineTo(this._x1,this._y1);break;case 3:Ct(this,this._t0,St(this,this._t0))}(this._line||0!==this._line&&1===this._point)&&this._context.closePath(),this._line=1-this._line},point:function(t,n){var e=NaN;if(t=+t,n=+n,t!==this._x1||n!==this._y1){switch(this._point){case 0:this._point=1,this._line?this._context.lineTo(t,n):this._context.moveTo(t,n);break;case 1:this._point=2;break;case 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t=this.originalEvent;this.isPropagationStopped=k,t&&!this.isSimulated&&t.stopPropagation()},stopImmediatePropagation:function(){var t=this.originalEvent;this.isImmediatePropagationStopped=k,t&&!this.isSimulated&&t.stopImmediatePropagation(),this.stopPropagation()}},mt.each({altKey:!0,bubbles:!0,cancelable:!0,changedTouches:!0,ctrlKey:!0,detail:!0,eventPhase:!0,metaKey:!0,pageX:!0,pageY:!0,shiftKey:!0,view:!0,char:!0,charCode:!0,key:!0,keyCode:!0,button:!0,buttons:!0,clientX:!0,clientY:!0,offsetX:!0,offsetY:!0,pointerId:!0,pointerType:!0,screenX:!0,screenY:!0,targetTouches:!0,toElement:!0,touches:!0,which:function(t){var n=t.button;return null==t.which&&nn.test(t.type)?null!=t.charCode?t.charCode:t.keyCode:!t.which&&void 0!==n&&en.test(t.type)?1&n?1:2&n?3:4&n?2:0:t.which}},mt.event.addProp),mt.each({mouseenter:"mouseover",mouseleave:"mouseout",pointerenter:"pointerover",pointerleave:"pointerout"},function(t,n){mt.event.special[t]={delegateType:n,bindType:n,handle:function(t){var e,r=this,i=t.relatedTarget,o=t.handleObj;return i&&(i===r||mt.contains(r,i))||(t.type=o.origType,e=o.handler.apply(this,arguments),t.type=n),e}}}),mt.fn.extend({on:function(t,n,e,r){return C(this,t,n,e,r)},one:function(t,n,e,r){return C(this,t,n,e,r,1)},off:function(t,n,e){var r,i;if(t&&t.preventDefault&&t.handleObj)return r=t.handleObj,mt(t.delegateTarget).off(r.namespace?r.origType+"."+r.namespace:r.origType,r.selector,r.handler),this;if("object"==typeof t){for(i in t)this.off(i,n,t[i]);return this}return n!==!1&&"function"!=typeof n||(e=n,n=void 0),e===!1&&(e=T),this.each(function(){mt.event.remove(this,t,e,n)})}});var on=/<(?!area|br|col|embed|hr|img|input|link|meta|param)(([a-z][^\/\0>\x20\t\r\n\f]*)[^>]*)\/>/gi,an=/<script|<style|<link/i,un=/checked\s*(?:[^=]|=\s*.checked.)/i,sn=/^true\/(.*)/,cn=/^\s*<!(?:\[CDATA\[|--)|(?:\]\]|--)>\s*$/g;mt.extend({htmlPrefilter:function(t){return t.replace(on,"<$1></$2>")},clone:function(t,n,e){var r,i,o,a,u=t.cloneNode(!0),s=mt.contains(t.ownerDocument,t);if(!(vt.noCloneChecked||1!==t.nodeType&&11!==t.nodeType||mt.isXMLDoc(t)))for(a=b(u),o=b(t),r=0,i=o.length;r<i;r++)D(o[r],a[r]);if(n)if(e)for(o=o||b(t),a=a||b(u),r=0,i=o.length;r<i;r++)q(o[r],a[r]);else q(t,u);return a=b(u,"script"),a.length>0&&w(a,!s&&b(t,"script")),u},cleanData:function(t){for(var n,e,r,i=mt.event.special,o=0;void 0!==(e=t[o]);o++)if(zt(e)){if(n=e[Rt.expando]){if(n.events)for(r in n.events)i[r]?mt.event.remove(e,r):mt.removeEvent(e,r,n.handle);e[Rt.expando]=void 0}e[Ht.expando]&&(e[Ht.expando]=void 0)}}}),mt.fn.extend({detach:function(t){return L(this,t,!0)},remove:function(t){return L(this,t)},text:function(t){return Ft(this,function(t){return void 0===t?mt.text(this):this.empty().each(function(){1!==this.nodeType&&11!==this.nodeType&&9!==this.nodeType||(this.textContent=t)})},null,t,arguments.length)},append:function(){return j(this,arguments,function(t){if(1===this.nodeType||11===this.nodeType||9===this.nodeType){var n=N(this,t);n.appendChild(t)}})},prepend:function(){return j(this,arguments,function(t){if(1===this.nodeType||11===this.nodeType||9===this.nodeType){var n=N(this,t);n.insertBefore(t,n.firstChild)}})},before:function(){return j(this,arguments,function(t){this.parentNode&&this.parentNode.insertBefore(t,this)})},after:function(){return j(this,arguments,function(t){this.parentNode&&this.parentNode.insertBefore(t,this.nextSibling)})},empty:function(){for(var t,n=0;null!=(t=this[n]);n++)1===t.nodeType&&(mt.cleanData(b(t,!1)),t.textContent="");return this},clone:function(t,n){return t=null!=t&&t,n=null==n?t:n,this.map(function(){return mt.clone(this,t,n)})},html:function(t){return Ft(this,function(t){var n=this[0]||{},e=0,r=this.length;if(void 0===t&&1===n.nodeType)return n.innerHTML;if("string"==typeof t&&!an.test(t)&&!Qt[(Jt.exec(t)||["",""])[1].toLowerCase()]){t=mt.htmlPrefilter(t);try{for(;e<r;e++)n=this[e]||{},1===n.nodeType&&(mt.cleanData(b(n,!1)),n.innerHTML=t);n=0}catch(t){}}n&&this.empty().append(t)},null,t,arguments.length)},replaceWith:function(){var t=[];return j(this,arguments,function(n){var e=this.parentNode;mt.inArray(this,t)<0&&(mt.cleanData(b(this)),e&&e.replaceChild(n,this))},t)}}),mt.each({appendTo:"append",prependTo:"prepend",insertBefore:"before",insertAfter:"after",replaceAll:"replaceWith"},function(t,n){mt.fn[t]=function(t){for(var e,r=[],i=mt(t),o=i.length-1,a=0;a<=o;a++)e=a===o?this:this.clone(!0),mt(i[a])[n](e),ct.apply(r,e.get());return this.pushStack(r)}});var ln=/^margin/,fn=new RegExp("^("+Bt+")(?!px)[a-z%]+$","i"),hn=function(t){var n=t.ownerDocument.defaultView;return n&&n.opener||(n=e),n.getComputedStyle(t)};!function(){function t(){if(u){u.style.cssText="box-sizing:border-box;position:relative;display:block;margin:auto;border:1px;padding:1px;top:1%;width:50%",u.innerHTML="",tn.appendChild(a);var t=e.getComputedStyle(u);n="1%"!==t.top,o="2px"===t.marginLeft,r="4px"===t.width,u.style.marginRight="50%",i="4px"===t.marginRight,tn.removeChild(a),u=null}}var n,r,i,o,a=ot.createElement("div"),u=ot.createElement("div");u.style&&(u.style.backgroundClip="content-box",u.cloneNode(!0).style.backgroundClip="",vt.clearCloneStyle="content-box"===u.style.backgroundClip,a.style.cssText="border:0;width:8px;height:0;top:0;left:-9999px;padding:0;margin-top:1px;position:absolute",a.appendChild(u),mt.extend(vt,{pixelPosition:function(){return t(),n},boxSizingReliable:function(){return t(),r},pixelMarginRight:function(){return t(),i},reliableMarginLeft:function(){return t(),o}}))}();var pn=/^(none|table(?!-c[ea]).+)/,dn={position:"absolute",visibility:"hidden",display:"block"},gn={letterSpacing:"0",fontWeight:"400"},vn=["Webkit","Moz","ms"],yn=ot.createElement("div").style;mt.extend({cssHooks:{opacity:{get:function(t,n){if(n){var e=P(t,"opacity");return""===e?"1":e}}}},cssNumber:{animationIterationCount:!0,columnCount:!0,fillOpacity:!0,flexGrow:!0,flexShrink:!0,fontWeight:!0,lineHeight:!0,opacity:!0,order:!0,orphans:!0,widows:!0,zIndex:!0,zoom:!0},cssProps:{float:"cssFloat"},style:function(t,n,e,r){if(t&&3!==t.nodeType&&8!==t.nodeType&&t.style){var i,o,a,u=mt.camelCase(n),s=t.style;return n=mt.cssProps[u]||(mt.cssProps[u]=F(u)||u),a=mt.cssHooks[n]||mt.cssHooks[u],void 0===e?a&&"get"in a&&void 0!==(i=a.get(t,!1,r))?i:s[n]:(o=typeof e,"string"===o&&(i=Wt.exec(e))&&i[1]&&(e=m(t,n,i),o="number"),null!=e&&e===e&&("number"===o&&(e+=i&&i[3]||(mt.cssNumber[u]?"":"px")),vt.clearCloneStyle||""!==e||0!==n.indexOf("background")||(s[n]="inherit"),a&&"set"in a&&void 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this.options.duration?this.pos=n=mt.easing[this.easing](t,this.options.duration*t,0,1,this.options.duration):this.pos=n=t,this.now=(this.end-this.start)*n+this.start,this.options.step&&this.options.step.call(this.elem,this.now,this),e&&e.set?e.set(this):I.propHooks._default.set(this),this}},I.prototype.init.prototype=I.prototype,I.propHooks={_default:{get:function(t){var n;return 1!==t.elem.nodeType||null!=t.elem[t.prop]&&null==t.elem.style[t.prop]?t.elem[t.prop]:(n=mt.css(t.elem,t.prop,""),n&&"auto"!==n?n:0)},set:function(t){mt.fx.step[t.prop]?mt.fx.step[t.prop](t):1!==t.elem.nodeType||null==t.elem.style[mt.cssProps[t.prop]]&&!mt.cssHooks[t.prop]?t.elem[t.prop]=t.now:mt.style(t.elem,t.prop,t.now+t.unit)}}},I.propHooks.scrollTop=I.propHooks.scrollLeft={set:function(t){t.elem.nodeType&&t.elem.parentNode&&(t.elem[t.prop]=t.now)}},mt.easing={linear:function(t){return t},swing:function(t){return.5-Math.cos(t*Math.PI)/2},_default:"swing"},mt.fx=I.prototype.init,mt.fx.step={};var mn,_n,xn=/^(?:toggle|show|hide)$/,bn=/queueHooks$/;mt.Animation=mt.extend(V,{tweeners:{"*":[function(t,n){var e=this.createTween(t,n);return m(e.elem,t,Wt.exec(n),e),e}]},tweener:function(t,n){mt.isFunction(t)?(n=t,t=["*"]):t=t.match(Lt);for(var e,r=0,i=t.length;r<i;r++)e=t[r],V.tweeners[e]=V.tweeners[e]||[],V.tweeners[e].unshift(n)},prefilters:[$],prefilter:function(t,n){n?V.prefilters.unshift(t):V.prefilters.push(t)}}),mt.speed=function(t,n,e){var r=t&&"object"==typeof t?mt.extend({},t):{complete:e||!e&&n||mt.isFunction(t)&&t,duration:t,easing:e&&n||n&&!mt.isFunction(n)&&n};return mt.fx.off||ot.hidden?r.duration=0:"number"!=typeof r.duration&&(r.duration in mt.fx.speeds?r.duration=mt.fx.speeds[r.duration]:r.duration=mt.fx.speeds._default),null!=r.queue&&r.queue!==!0||(r.queue="fx"),r.old=r.complete,r.complete=function(){mt.isFunction(r.old)&&r.old.call(this),r.queue&&mt.dequeue(this,r.queue)},r},mt.fn.extend({fadeTo:function(t,n,e,r){return 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0},mt.fx.timer=function(t){mt.timers.push(t),t()?mt.fx.start():mt.timers.pop()},mt.fx.interval=13,mt.fx.start=function(){_n||(_n=e.requestAnimationFrame?e.requestAnimationFrame(U):e.setInterval(mt.fx.tick,mt.fx.interval))},mt.fx.stop=function(){e.cancelAnimationFrame?e.cancelAnimationFrame(_n):e.clearInterval(_n),_n=null},mt.fx.speeds={slow:600,fast:200,_default:400},mt.fn.delay=function(t,n){return t=mt.fx?mt.fx.speeds[t]||t:t,n=n||"fx",this.queue(n,function(n,r){var i=e.setTimeout(n,t);r.stop=function(){e.clearTimeout(i)}})},function(){var t=ot.createElement("input"),n=ot.createElement("select"),e=n.appendChild(ot.createElement("option"));t.type="checkbox",vt.checkOn=""!==t.value,vt.optSelected=e.selected,t=ot.createElement("input"),t.value="t",t.type="radio",vt.radioValue="t"===t.value}();var wn,Mn=mt.expr.attrHandle;mt.fn.extend({attr:function(t,n){return Ft(this,mt.attr,t,n,arguments.length>1)},removeAttr:function(t){return 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n.color[1]-=n.color[1]*t,n},whiten:function(t){var n=this.hwb();return n.color[1]+=n.color[1]*t,n},blacken:function(t){var n=this.hwb();return n.color[2]+=n.color[2]*t,n},grayscale:function(){var t=this.rgb().color,n=.3*t[0]+.59*t[1]+.11*t[2];return r.rgb(n,n,n)},fade:function(t){return this.alpha(this.valpha-this.valpha*t)},opaquer:function(t){return this.alpha(this.valpha+this.valpha*t)},rotate:function(t){var n=this.hsl(),e=n.color[0];return e=(e+t)%360,e=e<0?360+e:e,n.color[0]=e,n},mix:function(t,n){var e=this.rgb(),i=t.rgb(),o=void 0===n?.5:n,a=2*o-1,u=e.alpha()-i.alpha(),s=((a*u===-1?a:(a+u)/(1+a*u))+1)/2,c=1-s;return r.rgb(s*e.red()+c*i.red(),s*e.green()+c*i.green(),s*e.blue()+c*i.blue(),e.alpha()*o+i.alpha()*(1-o))}},Object.keys(f).forEach(function(t){if(p.indexOf(t)===-1){var n=f[t].channels;r.prototype[t]=function(){if(this.model===t)return new r(this);if(arguments.length)return new r(arguments,t);var e="number"==typeof arguments[n]?n:this.valpha;return new 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if(n=t.match(a))for(n=n[1],e=0;e<3;e++){var f=2*e;l[e]=parseInt(n.slice(f,f+2),16)}else if(n=t.match(u)){for(e=0;e<3;e++)l[e]=parseInt(n[e+1],0);n[4]&&(l[3]=parseFloat(n[4]))}else if(n=t.match(s)){for(e=0;e<3;e++)l[e]=Math.round(2.55*parseFloat(n[e+1]));n[4]&&(l[3]=parseFloat(n[4]))}else if(n=t.match(c))return"transparent"===n[1]?[0,0,0,0]:(l=o[n[1]])?(l[3]=1,l):null;for(e=0;e<l.length;e++)l[e]=r(l[e],0,255);return l[3]=r(l[3],0,1),l},c.get.hsl=function(t){if(!t)return null;var n=/^hsla?\(\s*([+-]?\d*[\.]?\d+)(?:deg)?\s*,\s*([+-]?[\d\.]+)%\s*,\s*([+-]?[\d\.]+)%\s*(?:,\s*([+-]?[\d\.]+)\s*)?\)$/,e=t.match(n);if(e){var i=parseFloat(e[4]),o=(parseFloat(e[1])%360+360)%360,a=r(parseFloat(e[2]),0,100),u=r(parseFloat(e[3]),0,100),s=r(isNaN(i)?1:i,0,1);return[o,a,u,s]}return null},c.get.hwb=function(t){if(!t)return null;var n=/^hwb\(\s*([+-]?\d*[\.]?\d+)(?:deg)?\s*,\s*([+-]?[\d\.]+)%\s*,\s*([+-]?[\d\.]+)%\s*(?:,\s*([+-]?[\d\.]+)\s*)?\)$/,e=t.match(n);if(e){var 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--- a/cpt_xmfa/mauve.xml Tue Jul 05 05:07:32 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,69 +0,0 @@ -<?xml version="1.0"?> -<tool id="edu.tamu.cpt.comparative.mauve" name="X-Vis" version="1.0" profile="16.04"> - <description>from XMFA file</description> - <macros> - <import>macros.xml</import> - <import>cpt-macros.xml</import> - </macros> - <configfiles> - <configfile name="index"> - <![CDATA[ -#if ($frameHeight > 0): -<!DOCTYPE html> -<html lang="en"> -<head> - <meta charset="UTF-8"> - <meta name="viewport" content="width=device-width, height=$frameHeight, initial-scale=1"> - <meta name="description" content="X-Vis"> - <title>X-Vis</title> - <link rel="shortcut icon" href="favicon.ico"> -</head> -<body> - <script src="mauve.js"></script> -</body> -</html> -#else: -<!DOCTYPE html> -<html lang="en"> -<head> - <meta charset="UTF-8"> - <meta name="viewport" content="width=device-width, initial-scale=1"> - <meta name="description" content="X-Vis"> - <title>X-Vis</title> - <link rel="shortcut icon" href="favicon.ico"> -</head> -<body> - <script src="mauve.js"></script> -</body> -</html> -#end if - ]]> - </configfile> - </configfiles> - <expand macro="requirements"/> - <command detect_errors="aggressive"><![CDATA[ -@GENOME_SELECTOR_PRE@ -mkdir -p "$output.files_path"; - -python $__tool_directory__/xmfa_process.py -@INPUT_GFF@ -@INPUT_FASTA@ -@XMFA_INPUT@ -"out" > "$output.files_path/data.json"; -mv out "$output.files_path/"; - -cp $__tool_directory__/mauve.js $output.files_path/; -cp $index "$output" -]]></command> - <inputs> - <expand macro="input/gff3+fasta" /> - <expand macro="xmfa_input" /> - <param label="Manually Set Height (0 for auto-scaling)" name="frameHeight" type="integer" value="0"/> - </inputs> - <outputs> - <data format="html" name="output" /> - </outputs> - <help> - </help> - <tests/> -</tool>
--- a/cpt_xmfa/xmfa_process.py Tue Jul 05 05:07:32 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,118 +0,0 @@ -#!/usr/bin/env python -from Bio import SeqIO -import argparse -import json -import os -from CPT_GFFParser import gffParse, gffWrite - - -def parse_xmfa(xmfa): - """Simple XMFA parser until https://github.com/biopython/biopython/pull/544 - """ - current_lcb = [] - current_seq = {} - for line in xmfa.readlines(): - if line.startswith("#"): - continue - - if line.strip() == "=": - if "id" in current_seq: - current_lcb.append(current_seq) - current_seq = {} - yield current_lcb - current_lcb = [] - else: - line = line.strip() - if line.startswith(">"): - if "id" in current_seq: - current_lcb.append(current_seq) - current_seq = {} - data = line.strip().split() - # 0 1 2 3 4 5 - # > 1:5986-6406 + CbK.fa # CbK_gp011 - id, loc = data[1].split(":") - start, end = loc.split("-") - current_seq = { - "rid": "_".join(data[1:]), - "id": id, - "start": int(start), - "end": int(end), - "strand": 1 if data[2] == "+" else -1, - "seq": "", - "comment": "", - } - if len(data) > 5: - current_seq["comment"] = " ".join(data[5:]) - # else: - # current_seq['seq'] += line.strip() - - -def percent_identity(a, b): - """Calculate % identity, ignoring gaps in the host sequence - """ - match = 0 - mismatch = 0 - for char_a, char_b in zip(list(a), list(b)): - if char_a == "-": - continue - if char_a == char_b: - match += 1 - else: - mismatch += 1 - - if match + mismatch == 0: - return 0.0 - return 100 * float(match) / (match + mismatch) - - -def get_fasta_ids(sequences): - """Returns a list of fasta records in the order they appear - """ - ids = [] - for seq in SeqIO.parse(sequences, "fasta"): - ids.append(seq.id) - return ids - - -if __name__ == "__main__": - parser = argparse.ArgumentParser(description="parse xmfa file") - parser.add_argument("gff3", type=argparse.FileType("r"), help="Multi-GFF3 File") - parser.add_argument("fasta", type=argparse.FileType("r"), help="Multi-FA file") - parser.add_argument("xmfa", type=argparse.FileType("r"), help="XMFA File") - parser.add_argument("output_dir", type=str, help="output directory") - args = parser.parse_args() - - fasta_list = get_fasta_ids(args.fasta) - lcbs = parse_xmfa(args.xmfa) - - if not os.path.exists(args.output_dir): - os.makedirs(args.output_dir) - - output = {"fasta": [], "gff3": [], "xmfa": None} - - processed_xmfa = os.path.join(args.output_dir, "regions.json") - with open(processed_xmfa, "w") as handle: - json.dump([lcb for lcb in lcbs if len(lcb) > 1], handle, sort_keys=True) - - output["xmfa"] = processed_xmfa - - # Have to seek because we already access args.fasta once in id_tn_dict - args.fasta.seek(0) - # Load up sequence(s) for GFF3 data - seq_dict = SeqIO.to_dict(SeqIO.parse(args.fasta, "fasta")) - # Parse GFF3 records - gffs = gffParse(args.gff3, base_dict=seq_dict) - for record in sorted(gffs, key=lambda rec: fasta_list.index(rec.id)): - gff_output = os.path.join(args.output_dir, record.id + ".gff") - with open(gff_output, "w") as handle: - gffWrite([record], handle) - output["gff3"].append(gff_output) - - fa_output = os.path.join(args.output_dir, record.id + ".txt") - with open(fa_output, "w") as handle: - handle.write(str(record.seq)) - output["fasta"].append( - {"path": fa_output, "length": len(record.seq), "name": record.id} - ) - - print(json.dumps(output, sort_keys=True))
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jun 05 02:54:26 2023 +0000 @@ -0,0 +1,74 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package">progressivemauve</requirement> + <!--<requirement type="package" version="2.7">python</requirement>--> + <requirement type="package" version="0.6.4">bcbiogff</requirement> + <yield/> + </requirements> + </xml> + <token name="@WRAPPER_VERSION@">2.4.0</token> + <xml name="citation/progressive_mauve"> + <citation type="doi">10.1371/journal.pone.0011147</citation> + </xml> + <xml name="citation/gepard"> + <citation type="doi">10.1093/bioinformatics/btm039</citation> + </xml> + <token name="@XMFA_INPUT@"> + '$xmfa' + </token> + <xml name="xmfa_input" token_formats="xmfa"> + <param type="data" format="@FORMATS@" name="xmfa" label="XMFA MSA"/> + </xml> + <token name="@XMFA_FA_INPUT@"> + '$sequences' + </token> + <xml name="xmfa_fa_input"> + <param type="data" format="fasta" name="sequences" label="Sequences in alignment" help="These sequences should be the SAME DATASET that was used in the progressiveMauve run. Failing that, they should be provided in the same order as in original progressiveMauve run"/> + </xml> + <xml name="genome_selector"> + <conditional name="reference_genome"> + <param name="reference_genome_source" type="select" label="Reference Genome"> + <option value="history" selected="True">From History</option> + <option value="cached">Locally Cached</option> + </param> + <when value="cached"> + <param name="fasta_indexes" type="select" label="Source FASTA Sequence"> + <options from_data_table="all_fasta"/> + </param> + </when> + <when value="history"> + <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/> + </when> + </conditional> + </xml> + <xml name="gff3_input"> + <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/> + </xml> + <xml name="input/gff3+fasta"> + <expand macro="gff3_input"/> + <expand macro="genome_selector"/> + </xml> + <token name="@INPUT_GFF@"> + '$gff3_data' + </token> + <token name="@INPUT_FASTA@"> + #if str($reference_genome.reference_genome_source) == 'cached': + '${reference_genome.fasta_indexes.fields.path}' + #else if str($reference_genome.reference_genome_source) == 'history': + genomeref.fa + #end if + </token> + <token name="@GENOME_SELECTOR_PRE@"> + #if $reference_genome.reference_genome_source == 'history': + ln -s '$reference_genome.genome_fasta' genomeref.fa; + #end if + </token> + <token name="@GENOME_SELECTOR@"> + #if str($reference_genome.reference_genome_source) == 'cached': + '${reference_genome.fasta_indexes.fields.path}' + #else if str($reference_genome.reference_genome_source) == 'history': + genomeref.fa + #end if + </token> +</macros>
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n?new wt(t,n):new mt(t,0)}return e.alpha=function(n){return t(+n)},e}(.5);Mt.prototype={areaStart:Qf,areaEnd:Qf,lineStart:function(){this._point=0},lineEnd:function(){this._point&&this._context.closePath()},point:function(t,n){t=+t,n=+n,this._point?this._context.lineTo(t,n):(this._point=1,this._context.moveTo(t,n))}};var ch=function(t){return new Mt(t)};Nt.prototype={areaStart:function(){this._line=0},areaEnd:function(){this._line=NaN},lineStart:function(){this._x0=this._x1=this._y0=this._y1=this._t0=NaN,this._point=0},lineEnd:function(){switch(this._point){case 2:this._context.lineTo(this._x1,this._y1);break;case 3:Ct(this,this._t0,St(this,this._t0))}(this._line||0!==this._line&&1===this._point)&&this._context.closePath(),this._line=1-this._line},point:function(t,n){var e=NaN;if(t=+t,n=+n,t!==this._x1||n!==this._y1){switch(this._point){case 0:this._point=1,this._line?this._context.lineTo(t,n):this._context.moveTo(t,n);break;case 1:this._point=2;break;case 2:this._point=3,Ct(this,St(this,e=Tt(this,t,n)),e);break;default:Ct(this,this._t0,e=Tt(this,t,n))}this._x0=this._x1,this._x1=t,this._y0=this._y1,this._y1=n,this._t0=e}}},(Et.prototype=Object.create(Nt.prototype)).point=function(t,n){Nt.prototype.point.call(this,n,t)},At.prototype={moveTo:function(t,n){this._context.moveTo(n,t)},closePath:function(){this._context.closePath()},lineTo:function(t,n){this._context.lineTo(n,t)},bezierCurveTo:function(t,n,e,r,i,o){this._context.bezierCurveTo(n,t,r,e,o,i)}},jt.prototype={areaStart:function(){this._line=0},areaEnd:function(){this._line=NaN},lineStart:function(){this._x=[],this._y=[]},lineEnd:function(){var t=this._x,n=this._y,e=t.length;if(e)if(this._line?this._context.lineTo(t[0],n[0]):this._context.moveTo(t[0],n[0]),2===e)this._context.lineTo(t[1],n[1]);else for(var 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t=this.originalEvent;this.isPropagationStopped=k,t&&!this.isSimulated&&t.stopPropagation()},stopImmediatePropagation:function(){var t=this.originalEvent;this.isImmediatePropagationStopped=k,t&&!this.isSimulated&&t.stopImmediatePropagation(),this.stopPropagation()}},mt.each({altKey:!0,bubbles:!0,cancelable:!0,changedTouches:!0,ctrlKey:!0,detail:!0,eventPhase:!0,metaKey:!0,pageX:!0,pageY:!0,shiftKey:!0,view:!0,char:!0,charCode:!0,key:!0,keyCode:!0,button:!0,buttons:!0,clientX:!0,clientY:!0,offsetX:!0,offsetY:!0,pointerId:!0,pointerType:!0,screenX:!0,screenY:!0,targetTouches:!0,toElement:!0,touches:!0,which:function(t){var n=t.button;return null==t.which&&nn.test(t.type)?null!=t.charCode?t.charCode:t.keyCode:!t.which&&void 0!==n&&en.test(t.type)?1&n?1:2&n?3:4&n?2:0:t.which}},mt.event.addProp),mt.each({mouseenter:"mouseover",mouseleave:"mouseout",pointerenter:"pointerover",pointerleave:"pointerout"},function(t,n){mt.event.special[t]={delegateType:n,bindType:n,handle:function(t){var e,r=this,i=t.relatedTarget,o=t.handleObj;return i&&(i===r||mt.contains(r,i))||(t.type=o.origType,e=o.handler.apply(this,arguments),t.type=n),e}}}),mt.fn.extend({on:function(t,n,e,r){return C(this,t,n,e,r)},one:function(t,n,e,r){return C(this,t,n,e,r,1)},off:function(t,n,e){var r,i;if(t&&t.preventDefault&&t.handleObj)return r=t.handleObj,mt(t.delegateTarget).off(r.namespace?r.origType+"."+r.namespace:r.origType,r.selector,r.handler),this;if("object"==typeof t){for(i in t)this.off(i,n,t[i]);return this}return n!==!1&&"function"!=typeof n||(e=n,n=void 0),e===!1&&(e=T),this.each(function(){mt.event.remove(this,t,e,n)})}});var on=/<(?!area|br|col|embed|hr|img|input|link|meta|param)(([a-z][^\/\0>\x20\t\r\n\f]*)[^>]*)\/>/gi,an=/<script|<style|<link/i,un=/checked\s*(?:[^=]|=\s*.checked.)/i,sn=/^true\/(.*)/,cn=/^\s*<!(?:\[CDATA\[|--)|(?:\]\]|--)>\s*$/g;mt.extend({htmlPrefilter:function(t){return t.replace(on,"<$1></$2>")},clone:function(t,n,e){var r,i,o,a,u=t.cloneNode(!0),s=mt.contains(t.ownerDocument,t);if(!(vt.noCloneChecked||1!==t.nodeType&&11!==t.nodeType||mt.isXMLDoc(t)))for(a=b(u),o=b(t),r=0,i=o.length;r<i;r++)D(o[r],a[r]);if(n)if(e)for(o=o||b(t),a=a||b(u),r=0,i=o.length;r<i;r++)q(o[r],a[r]);else q(t,u);return a=b(u,"script"),a.length>0&&w(a,!s&&b(t,"script")),u},cleanData:function(t){for(var n,e,r,i=mt.event.special,o=0;void 0!==(e=t[o]);o++)if(zt(e)){if(n=e[Rt.expando]){if(n.events)for(r in n.events)i[r]?mt.event.remove(e,r):mt.removeEvent(e,r,n.handle);e[Rt.expando]=void 0}e[Ht.expando]&&(e[Ht.expando]=void 0)}}}),mt.fn.extend({detach:function(t){return L(this,t,!0)},remove:function(t){return L(this,t)},text:function(t){return Ft(this,function(t){return void 0===t?mt.text(this):this.empty().each(function(){1!==this.nodeType&&11!==this.nodeType&&9!==this.nodeType||(this.textContent=t)})},null,t,arguments.length)},append:function(){return j(this,arguments,function(t){if(1===this.nodeType||11===this.nodeType||9===this.nodeType){var n=N(this,t);n.appendChild(t)}})},prepend:function(){return j(this,arguments,function(t){if(1===this.nodeType||11===this.nodeType||9===this.nodeType){var n=N(this,t);n.insertBefore(t,n.firstChild)}})},before:function(){return j(this,arguments,function(t){this.parentNode&&this.parentNode.insertBefore(t,this)})},after:function(){return j(this,arguments,function(t){this.parentNode&&this.parentNode.insertBefore(t,this.nextSibling)})},empty:function(){for(var t,n=0;null!=(t=this[n]);n++)1===t.nodeType&&(mt.cleanData(b(t,!1)),t.textContent="");return this},clone:function(t,n){return t=null!=t&&t,n=null==n?t:n,this.map(function(){return mt.clone(this,t,n)})},html:function(t){return Ft(this,function(t){var n=this[0]||{},e=0,r=this.length;if(void 0===t&&1===n.nodeType)return n.innerHTML;if("string"==typeof t&&!an.test(t)&&!Qt[(Jt.exec(t)||["",""])[1].toLowerCase()]){t=mt.htmlPrefilter(t);try{for(;e<r;e++)n=this[e]||{},1===n.nodeType&&(mt.cleanData(b(n,!1)),n.innerHTML=t);n=0}catch(t){}}n&&this.empty().append(t)},null,t,arguments.length)},replaceWith:function(){var t=[];return j(this,arguments,function(n){var e=this.parentNode;mt.inArray(this,t)<0&&(mt.cleanData(b(this)),e&&e.replaceChild(n,this))},t)}}),mt.each({appendTo:"append",prependTo:"prepend",insertBefore:"before",insertAfter:"after",replaceAll:"replaceWith"},function(t,n){mt.fn[t]=function(t){for(var e,r=[],i=mt(t),o=i.length-1,a=0;a<=o;a++)e=a===o?this:this.clone(!0),mt(i[a])[n](e),ct.apply(r,e.get());return this.pushStack(r)}});var ln=/^margin/,fn=new RegExp("^("+Bt+")(?!px)[a-z%]+$","i"),hn=function(t){var n=t.ownerDocument.defaultView;return n&&n.opener||(n=e),n.getComputedStyle(t)};!function(){function t(){if(u){u.style.cssText="box-sizing:border-box;position:relative;display:block;margin:auto;border:1px;padding:1px;top:1%;width:50%",u.innerHTML="",tn.appendChild(a);var t=e.getComputedStyle(u);n="1%"!==t.top,o="2px"===t.marginLeft,r="4px"===t.width,u.style.marginRight="50%",i="4px"===t.marginRight,tn.removeChild(a),u=null}}var n,r,i,o,a=ot.createElement("div"),u=ot.createElement("div");u.style&&(u.style.backgroundClip="content-box",u.cloneNode(!0).style.backgroundClip="",vt.clearCloneStyle="content-box"===u.style.backgroundClip,a.style.cssText="border:0;width:8px;height:0;top:0;left:-9999px;padding:0;margin-top:1px;position:absolute",a.appendChild(u),mt.extend(vt,{pixelPosition:function(){return t(),n},boxSizingReliable:function(){return t(),r},pixelMarginRight:function(){return t(),i},reliableMarginLeft:function(){return t(),o}}))}();var pn=/^(none|table(?!-c[ea]).+)/,dn={position:"absolute",visibility:"hidden",display:"block"},gn={letterSpacing:"0",fontWeight:"400"},vn=["Webkit","Moz","ms"],yn=ot.createElement("div").style;mt.extend({cssHooks:{opacity:{get:function(t,n){if(n){var e=P(t,"opacity");return""===e?"1":e}}}},cssNumber:{animationIterationCount:!0,columnCount:!0,fillOpacity:!0,flexGrow:!0,flexShrink:!0,fontWeight:!0,lineHeight:!0,opacity:!0,order:!0,orphans:!0,widows:!0,zIndex:!0,zoom:!0},cssProps:{float:"cssFloat"},style:function(t,n,e,r){if(t&&3!==t.nodeType&&8!==t.nodeType&&t.style){var i,o,a,u=mt.camelCase(n),s=t.style;return n=mt.cssProps[u]||(mt.cssProps[u]=F(u)||u),a=mt.cssHooks[n]||mt.cssHooks[u],void 0===e?a&&"get"in a&&void 0!==(i=a.get(t,!1,r))?i:s[n]:(o=typeof e,"string"===o&&(i=Wt.exec(e))&&i[1]&&(e=m(t,n,i),o="number"),null!=e&&e===e&&("number"===o&&(e+=i&&i[3]||(mt.cssNumber[u]?"":"px")),vt.clearCloneStyle||""!==e||0!==n.indexOf("background")||(s[n]="inherit"),a&&"set"in a&&void 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this.options.duration?this.pos=n=mt.easing[this.easing](t,this.options.duration*t,0,1,this.options.duration):this.pos=n=t,this.now=(this.end-this.start)*n+this.start,this.options.step&&this.options.step.call(this.elem,this.now,this),e&&e.set?e.set(this):I.propHooks._default.set(this),this}},I.prototype.init.prototype=I.prototype,I.propHooks={_default:{get:function(t){var n;return 1!==t.elem.nodeType||null!=t.elem[t.prop]&&null==t.elem.style[t.prop]?t.elem[t.prop]:(n=mt.css(t.elem,t.prop,""),n&&"auto"!==n?n:0)},set:function(t){mt.fx.step[t.prop]?mt.fx.step[t.prop](t):1!==t.elem.nodeType||null==t.elem.style[mt.cssProps[t.prop]]&&!mt.cssHooks[t.prop]?t.elem[t.prop]=t.now:mt.style(t.elem,t.prop,t.now+t.unit)}}},I.propHooks.scrollTop=I.propHooks.scrollLeft={set:function(t){t.elem.nodeType&&t.elem.parentNode&&(t.elem[t.prop]=t.now)}},mt.easing={linear:function(t){return t},swing:function(t){return.5-Math.cos(t*Math.PI)/2},_default:"swing"},mt.fx=I.prototype.init,mt.fx.step={};var mn,_n,xn=/^(?:toggle|show|hide)$/,bn=/queueHooks$/;mt.Animation=mt.extend(V,{tweeners:{"*":[function(t,n){var e=this.createTween(t,n);return m(e.elem,t,Wt.exec(n),e),e}]},tweener:function(t,n){mt.isFunction(t)?(n=t,t=["*"]):t=t.match(Lt);for(var e,r=0,i=t.length;r<i;r++)e=t[r],V.tweeners[e]=V.tweeners[e]||[],V.tweeners[e].unshift(n)},prefilters:[$],prefilter:function(t,n){n?V.prefilters.unshift(t):V.prefilters.push(t)}}),mt.speed=function(t,n,e){var r=t&&"object"==typeof t?mt.extend({},t):{complete:e||!e&&n||mt.isFunction(t)&&t,duration:t,easing:e&&n||n&&!mt.isFunction(n)&&n};return mt.fx.off||ot.hidden?r.duration=0:"number"!=typeof r.duration&&(r.duration in mt.fx.speeds?r.duration=mt.fx.speeds[r.duration]:r.duration=mt.fx.speeds._default),null!=r.queue&&r.queue!==!0||(r.queue="fx"),r.old=r.complete,r.complete=function(){mt.isFunction(r.old)&&r.old.call(this),r.queue&&mt.dequeue(this,r.queue)},r},mt.fn.extend({fadeTo:function(t,n,e,r){return 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0},mt.fx.timer=function(t){mt.timers.push(t),t()?mt.fx.start():mt.timers.pop()},mt.fx.interval=13,mt.fx.start=function(){_n||(_n=e.requestAnimationFrame?e.requestAnimationFrame(U):e.setInterval(mt.fx.tick,mt.fx.interval))},mt.fx.stop=function(){e.cancelAnimationFrame?e.cancelAnimationFrame(_n):e.clearInterval(_n),_n=null},mt.fx.speeds={slow:600,fast:200,_default:400},mt.fn.delay=function(t,n){return t=mt.fx?mt.fx.speeds[t]||t:t,n=n||"fx",this.queue(n,function(n,r){var i=e.setTimeout(n,t);r.stop=function(){e.clearTimeout(i)}})},function(){var t=ot.createElement("input"),n=ot.createElement("select"),e=n.appendChild(ot.createElement("option"));t.type="checkbox",vt.checkOn=""!==t.value,vt.optSelected=e.selected,t=ot.createElement("input"),t.value="t",t.type="radio",vt.radioValue="t"===t.value}();var wn,Mn=mt.expr.attrHandle;mt.fn.extend({attr:function(t,n){return Ft(this,mt.attr,t,n,arguments.length>1)},removeAttr:function(t){return 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n.color[1]-=n.color[1]*t,n},whiten:function(t){var n=this.hwb();return n.color[1]+=n.color[1]*t,n},blacken:function(t){var n=this.hwb();return n.color[2]+=n.color[2]*t,n},grayscale:function(){var t=this.rgb().color,n=.3*t[0]+.59*t[1]+.11*t[2];return r.rgb(n,n,n)},fade:function(t){return this.alpha(this.valpha-this.valpha*t)},opaquer:function(t){return this.alpha(this.valpha+this.valpha*t)},rotate:function(t){var n=this.hsl(),e=n.color[0];return e=(e+t)%360,e=e<0?360+e:e,n.color[0]=e,n},mix:function(t,n){var e=this.rgb(),i=t.rgb(),o=void 0===n?.5:n,a=2*o-1,u=e.alpha()-i.alpha(),s=((a*u===-1?a:(a+u)/(1+a*u))+1)/2,c=1-s;return r.rgb(s*e.red()+c*i.red(),s*e.green()+c*i.green(),s*e.blue()+c*i.blue(),e.alpha()*o+i.alpha()*(1-o))}},Object.keys(f).forEach(function(t){if(p.indexOf(t)===-1){var n=f[t].channels;r.prototype[t]=function(){if(this.model===t)return new r(this);if(arguments.length)return new r(arguments,t);var e="number"==typeof arguments[n]?n:this.valpha;return new 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if(n=t.match(a))for(n=n[1],e=0;e<3;e++){var f=2*e;l[e]=parseInt(n.slice(f,f+2),16)}else if(n=t.match(u)){for(e=0;e<3;e++)l[e]=parseInt(n[e+1],0);n[4]&&(l[3]=parseFloat(n[4]))}else if(n=t.match(s)){for(e=0;e<3;e++)l[e]=Math.round(2.55*parseFloat(n[e+1]));n[4]&&(l[3]=parseFloat(n[4]))}else if(n=t.match(c))return"transparent"===n[1]?[0,0,0,0]:(l=o[n[1]])?(l[3]=1,l):null;for(e=0;e<l.length;e++)l[e]=r(l[e],0,255);return l[3]=r(l[3],0,1),l},c.get.hsl=function(t){if(!t)return null;var n=/^hsla?\(\s*([+-]?\d*[\.]?\d+)(?:deg)?\s*,\s*([+-]?[\d\.]+)%\s*,\s*([+-]?[\d\.]+)%\s*(?:,\s*([+-]?[\d\.]+)\s*)?\)$/,e=t.match(n);if(e){var i=parseFloat(e[4]),o=(parseFloat(e[1])%360+360)%360,a=r(parseFloat(e[2]),0,100),u=r(parseFloat(e[3]),0,100),s=r(isNaN(i)?1:i,0,1);return[o,a,u,s]}return null},c.get.hwb=function(t){if(!t)return null;var n=/^hwb\(\s*([+-]?\d*[\.]?\d+)(?:deg)?\s*,\s*([+-]?[\d\.]+)%\s*,\s*([+-]?[\d\.]+)%\s*(?:,\s*([+-]?[\d\.]+)\s*)?\)$/,e=t.match(n);if(e){var 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mauve.xml Mon Jun 05 02:54:26 2023 +0000 @@ -0,0 +1,68 @@ +<tool id="edu.tamu.cpt.comparative.mauve" name="X-Vis" version="1.0" profile="16.04"> + <description>from XMFA file</description> + <macros> + <import>macros.xml</import> + <import>cpt-macros.xml</import> + </macros> + <configfiles> + <configfile name="index"> + <![CDATA[ +#if ($frameHeight > 0): +<!DOCTYPE html> +<html lang="en"> +<head> + <meta charset="UTF-8"> + <meta name="viewport" content="width=device-width, height=$frameHeight, initial-scale=1"> + <meta name="description" content="X-Vis"> + <title>X-Vis</title> + <link rel="shortcut icon" href="favicon.ico"> +</head> +<body> + <script src="mauve.js"></script> +</body> +</html> +#else: +<!DOCTYPE html> +<html lang="en"> +<head> + <meta charset="UTF-8"> + <meta name="viewport" content="width=device-width, initial-scale=1"> + <meta name="description" content="X-Vis"> + <title>X-Vis</title> + <link rel="shortcut icon" href="favicon.ico"> +</head> +<body> + <script src="mauve.js"></script> +</body> +</html> +#end if + ]]> + </configfile> + </configfiles> + <expand macro="requirements"/> + <command detect_errors="aggressive"><![CDATA[ +@GENOME_SELECTOR_PRE@ +mkdir -p "$output.files_path"; + +python '$__tool_directory__/xmfa_process.py' +@INPUT_GFF@ +@INPUT_FASTA@ +@XMFA_INPUT@ +"out" > "$output.files_path/data.json"; +mv out "$output.files_path/"; + +cp '$__tool_directory__/mauve.js' '$output.files_path/'; +cp '$index' "$output" +]]></command> + <inputs> + <expand macro="input/gff3+fasta"/> + <expand macro="xmfa_input"/> + <param label="Manually Set Height (0 for auto-scaling)" name="frameHeight" type="integer" value="0"/> + </inputs> + <outputs> + <data format="html" name="output"/> + </outputs> + <help> + </help> + <tests/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/xmfa_process.py Mon Jun 05 02:54:26 2023 +0000 @@ -0,0 +1,115 @@ +#!/usr/bin/env python +from Bio import SeqIO +import argparse +import json +import os +from CPT_GFFParser import gffParse, gffWrite + + +def parse_xmfa(xmfa): + """Simple XMFA parser until https://github.com/biopython/biopython/pull/544""" + current_lcb = [] + current_seq = {} + for line in xmfa.readlines(): + if line.startswith("#"): + continue + + if line.strip() == "=": + if "id" in current_seq: + current_lcb.append(current_seq) + current_seq = {} + yield current_lcb + current_lcb = [] + else: + line = line.strip() + if line.startswith(">"): + if "id" in current_seq: + current_lcb.append(current_seq) + current_seq = {} + data = line.strip().split() + # 0 1 2 3 4 5 + # > 1:5986-6406 + CbK.fa # CbK_gp011 + id, loc = data[1].split(":") + start, end = loc.split("-") + current_seq = { + "rid": "_".join(data[1:]), + "id": id, + "start": int(start), + "end": int(end), + "strand": 1 if data[2] == "+" else -1, + "seq": "", + "comment": "", + } + if len(data) > 5: + current_seq["comment"] = " ".join(data[5:]) + # else: + # current_seq['seq'] += line.strip() + + +def percent_identity(a, b): + """Calculate % identity, ignoring gaps in the host sequence""" + match = 0 + mismatch = 0 + for char_a, char_b in zip(list(a), list(b)): + if char_a == "-": + continue + if char_a == char_b: + match += 1 + else: + mismatch += 1 + + if match + mismatch == 0: + return 0.0 + return 100 * float(match) / (match + mismatch) + + +def get_fasta_ids(sequences): + """Returns a list of fasta records in the order they appear""" + ids = [] + for seq in SeqIO.parse(sequences, "fasta"): + ids.append(seq.id) + return ids + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="parse xmfa file") + parser.add_argument("gff3", type=argparse.FileType("r"), help="Multi-GFF3 File") + parser.add_argument("fasta", type=argparse.FileType("r"), help="Multi-FA file") + parser.add_argument("xmfa", type=argparse.FileType("r"), help="XMFA File") + parser.add_argument("output_dir", type=str, help="output directory") + args = parser.parse_args() + + fasta_list = get_fasta_ids(args.fasta) + lcbs = parse_xmfa(args.xmfa) + + if not os.path.exists(args.output_dir): + os.makedirs(args.output_dir) + + output = {"fasta": [], "gff3": [], "xmfa": None} + + processed_xmfa = os.path.join(args.output_dir, "regions.json") + with open(processed_xmfa, "w") as handle: + json.dump([lcb for lcb in lcbs if len(lcb) > 1], handle, sort_keys=True) + + output["xmfa"] = processed_xmfa + + # Have to seek because we already access args.fasta once in id_tn_dict + args.fasta.seek(0) + # Load up sequence(s) for GFF3 data + seq_dict = SeqIO.to_dict(SeqIO.parse(args.fasta, "fasta")) + # Parse GFF3 records + gffs = gffParse(args.gff3, base_dict=seq_dict) + for record in sorted(gffs, key=lambda rec: fasta_list.index(rec.id)): + gff_output = os.path.join(args.output_dir, record.id + ".gff") + with open(gff_output, "w") as handle: + gffWrite([record], handle) + output["gff3"].append(gff_output) + + fa_output = os.path.join(args.output_dir, record.id + ".txt") + with open(fa_output, "w") as handle: + handle.write(str(record.seq)) + output["fasta"].append( + {"path": fa_output, "length": len(record.seq), "name": record.id} + ) + + print(json.dumps(output, sort_keys=True))