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Merged my most recent changes with the head from security.
This commit is contained in:
Nate Coraor
@@ -322,3 +322,6 @@ div.debug
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display: none;
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}
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pre {
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font-size: 80%;
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}
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@@ -60,13 +60,13 @@
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<td colspan="5">Stderr</td>
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</tr>
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<tr>
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<td colspan="5">${job[9]}</td>
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<td colspan="5"><pre>${job[9]}</pre></td>
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</tr>
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<tr class="header">
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<td colspan="5">Stack Trace</td>
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</tr>
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<tr>
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<td colspan="5">${job[10]}</td>
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<td colspan="5"><pre>${job[10]}</pre></td>
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</tr>
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<tr class="header">
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<td colspan="5">Info</td>
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@@ -64,13 +64,13 @@
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<td colspan="5">Stderr</td>
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</tr>
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<tr>
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<td colspan="5">${job[9]}</td>
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<td colspan="5"><pre>${job[9]}</pre></td>
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</tr>
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<tr class="header">
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<td colspan="5">Stack Trace</td>
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</tr>
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<tr>
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<td colspan="5">${job[10]}</td>
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<td colspan="5"><pre>${job[10]}</pre></td>
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</tr>
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<tr class="header">
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<td colspan="5">Info</td>
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@@ -51,13 +51,13 @@
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<td colspan="5">Stderr</td>
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</tr>
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<tr>
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<td colspan="5">${job[9]}</td>
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<td colspan="5"><pre>${job[9]}</pre></td>
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</tr>
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<tr class="header">
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<td colspan="5">Stack Trace</td>
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</tr>
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<tr>
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<td colspan="5">${job[10]}</td>
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<td colspan="5"><pre>${job[10]}</pre></td>
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</tr>
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<tr class="header">
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<td colspan="5">Info</td>
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@@ -64,13 +64,13 @@
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<td colspan="5">Stderr</td>
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</tr>
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<tr>
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<td colspan="5">${job[9]}</td>
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<td colspan="5"><pre>${job[9]}</pre></td>
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</tr>
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<tr class="header">
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<td colspan="5">Stack Trace</td>
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</tr>
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<tr>
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<td colspan="5">${job[10]}</td>
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<td colspan="5"><pre>${job[10]}</pre></td>
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</tr>
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<tr class="header">
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<td colspan="5">Info</td>
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@@ -64,13 +64,13 @@
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<td colspan="5">Stderr</td>
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</tr>
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<tr>
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<td colspan="5">${job[9]}</td>
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<td colspan="5"><pre>${job[9]}</pre></td>
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</tr>
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<tr class="header">
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<td colspan="5">Stack Trace</td>
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</tr>
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<tr>
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<td colspan="5">${job[10]}</td>
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<td colspan="5"><pre>${job[10]}</pre></td>
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</tr>
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<tr class="header">
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<td colspan="5">Info</td>
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File diff suppressed because one or more lines are too long
File diff suppressed because one or more lines are too long
@@ -1 +1 @@
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function CookieSet(A){this.cookie_name=A;this.store=store={};q.each((q.cookie(A)||"").split("|"),function(C,B){store[B]=true})}CookieSet.prototype.add=function(A){this.store[A]=true;return this};CookieSet.prototype.remove=function(A){delete this.store[A];return this};CookieSet.prototype.removeAll=function(A){this.store={};return this};CookieSet.prototype.contains=function(A){return(A in this.store)};CookieSet.prototype.save=function(){t=[];for(key in this.store){if(key!=""){t.push(key)}}q.cookie(this.cookie_name,t.join("|"));return this}
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function CookieSet(A){this.cookie_name=A;this.store=store={};q.each((q.cookie(A)||"").split("|"),function(C,B){store[B]=true})}CookieSet.prototype.add=function(A){this.store[A]=true;return this};CookieSet.prototype.remove=function(A){delete this.store[A];return this};CookieSet.prototype.removeAll=function(A){this.store={};return this};CookieSet.prototype.contains=function(A){return(A in this.store)};CookieSet.prototype.save=function(){t=[];for(key in this.store){if(key!=""){t.push(key)}}q.cookie(this.cookie_name,t.join("|"));return this};
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@@ -1 +1 @@
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jQuery(document).ready(function(){jQuery("a[@confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))})})
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@@ -1 +1 @@
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@@ -1 +1 @@
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File diff suppressed because one or more lines are too long
@@ -1,2 +1 @@
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(function(){if(!IE7.loaded){return }CLASSES=/\sie7_class\d+/g;IE7.CSS.extend({elements:{},handlers:[],reset:function(){this.removeEventHandlers();var elements=this.elements;for(var i in elements){elements[i].runtimeStyle.cssText=""}this.elements={};var elements=IE7.Rule.elements;for(var i in elements){with(elements[i]){className=className.replace(CLASSES,"")}}IE7.Rule.elements={}},reload:function(){this.rules=[];this.getInlineStyles();this.screen.load();if(this.print){this.print.load()}this.refresh();this.trash()},addRecalc:function(propertyName,test,handler,replacement){this.base(propertyName,test,function(element){handler(element);IE7.CSS.elements[element.uniqueID]=element},replacement)},recalc:function(){this.reset();this.base()},addEventHandler:function(element,type,handler){element.attachEvent(type,handler);this.handlers.push(arguments)},removeEventHandlers:function(){var handler;while(handler=this.handlers.pop()){handler[0].detachEvent(handler[1],handler[2])}},getInlineStyles:function(){var styleSheets=document.getElementsByTagName("style"),styleSheet;for(var i=styleSheets.length-1;(styleSheet=styleSheets[i]);i--){if(!styleSheet.disabled&&!styleSheet.ie7){var cssText=styleSheet.cssText||styleSheet.innerHTML;this.styles.push(cssText);styleSheet.cssText=cssText}}},trash:function(){var styleSheets=document.styleSheets,styleSheet,i;for(i=0;i<styleSheets.length;i++){styleSheet=styleSheets[i];if(!styleSheet.ie7&&!styleSheet.cssText){styleSheet.cssText=styleSheet.cssText}}this.base()},getText:function(styleSheet){return styleSheet.cssText||this.base(styleSheet)}});IE7.CSS.addEventHandler(window,"onunload",function(){IE7.CSS.removeEventHandlers()});IE7.Rule.elements={};IE7.Rule.prototype.extend({add:function(element){this.base(element);IE7.Rule.elements[element.uniqueID]=element}});if(IE7.PseudoElement){IE7.PseudoElement.hash={};IE7.PseudoElement.prototype.extend({create:function(target){var key=this.selector+":"+target.uniqueID;if(!IE7.PseudoElement.hash[key]){IE7.PseudoElement.hash[key]=true;this.base(target)}}})}IE7.HTML.extend({elements:{},addRecalc:function(selector,handler){this.base(selector,function(element){if(!this.elements[element.uniqueID]){handler(element);this.elements[element.uniqueID]=element}})}});document.recalc=function(reload){if(IE7.CSS.screen){if(reload){IE7.CSS.reload()}IE7.recalc()}}})();
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jQuery.cookie=function(B,I,L){if(typeof I!="undefined"){L=L||{};if(I===null){I="";L.expires=-1}var E="";if(L.expires&&(typeof L.expires=="number"||L.expires.toUTCString)){var F;if(typeof L.expires=="number"){F=new Date();F.setTime(F.getTime()+(L.expires*24*60*60*1000))}else{F=L.expires}E="; expires="+F.toUTCString()}var K=L.path?"; path="+L.path:"";var G=L.domain?"; domain="+L.domain:"";var A=L.secure?"; secure":"";document.cookie=[B,"=",encodeURIComponent(I),E,K,G,A].join("")}else{var D=null;if(document.cookie&&document.cookie!=""){var J=document.cookie.split(";");for(var H=0;H<J.length;H++){var C=jQuery.trim(J[H]);if(C.substring(0,B.length+1)==(B+"=")){D=decodeURIComponent(C.substring(B.length+1));break}}}return D}}
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jQuery.cookie=function(B,I,L){if(typeof I!="undefined"){L=L||{};if(I===null){I="";L.expires=-1}var E="";if(L.expires&&(typeof L.expires=="number"||L.expires.toUTCString)){var F;if(typeof L.expires=="number"){F=new Date();F.setTime(F.getTime()+(L.expires*24*60*60*1000))}else{F=L.expires}E="; expires="+F.toUTCString()}var K=L.path?"; path="+L.path:"";var G=L.domain?"; domain="+L.domain:"";var A=L.secure?"; secure":"";document.cookie=[B,"=",encodeURIComponent(I),E,K,G,A].join("")}else{var D=null;if(document.cookie&&document.cookie!=""){var J=document.cookie.split(";");for(var H=0;H<J.length;H++){var C=jQuery.trim(J[H]);if(C.substring(0,B.length+1)==(B+"=")){D=decodeURIComponent(C.substring(B.length+1));break}}}return D}};
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(function(A){A.fn.hoverIntent=function(I,H){var J={sensitivity:7,interval:100,timeout:0};J=A.extend(J,H?{over:I,out:H}:I);var L,K,F,D;var E=function(M){L=M.pageX;K=M.pageY};var C=function(N,M){M.hoverIntent_t=clearTimeout(M.hoverIntent_t);if((Math.abs(F-L)+Math.abs(D-K))<J.sensitivity){A(M).unbind("mousemove",E);M.hoverIntent_s=1;return J.over.apply(M,[N])}else{F=L;D=K;M.hoverIntent_t=setTimeout(function(){C(N,M)},J.interval)}};var G=function(N,M){M.hoverIntent_t=clearTimeout(M.hoverIntent_t);M.hoverIntent_s=0;return J.out.apply(M,[N])};var B=function(P){var O=(P.type=="mouseover"?P.fromElement:P.toElement)||P.relatedTarget;while(O&&O!=this){try{O=O.parentNode}catch(P){O=this}}if(O==this){return false}var N=A.extend({},P);var M=this;if(M.hoverIntent_t){M.hoverIntent_t=clearTimeout(M.hoverIntent_t)}if(P.type=="mouseover"){F=N.pageX;D=N.pageY;A(M).bind("mousemove",E);if(M.hoverIntent_s!=1){M.hoverIntent_t=setTimeout(function(){C(N,M)},J.interval)}}else{A(M).unbind("mousemove",E);if(M.hoverIntent_s==1){M.hoverIntent_t=setTimeout(function(){G(N,M)},J.timeout)}}};return this.mouseover(B).mouseout(B)}})(jQuery)
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(function(A){A.fn.hoverIntent=function(I,H){var J={sensitivity:7,interval:100,timeout:0};J=A.extend(J,H?{over:I,out:H}:I);var L,K,F,D;var E=function(M){L=M.pageX;K=M.pageY};var C=function(N,M){M.hoverIntent_t=clearTimeout(M.hoverIntent_t);if((Math.abs(F-L)+Math.abs(D-K))<J.sensitivity){A(M).unbind("mousemove",E);M.hoverIntent_s=1;return J.over.apply(M,[N])}else{F=L;D=K;M.hoverIntent_t=setTimeout(function(){C(N,M)},J.interval)}};var G=function(N,M){M.hoverIntent_t=clearTimeout(M.hoverIntent_t);M.hoverIntent_s=0;return J.out.apply(M,[N])};var B=function(P){var O=(P.type=="mouseover"?P.fromElement:P.toElement)||P.relatedTarget;while(O&&O!=this){try{O=O.parentNode}catch(P){O=this}}if(O==this){return false}var N=A.extend({},P);var M=this;if(M.hoverIntent_t){M.hoverIntent_t=clearTimeout(M.hoverIntent_t)}if(P.type=="mouseover"){F=N.pageX;D=N.pageY;A(M).bind("mousemove",E);if(M.hoverIntent_s!=1){M.hoverIntent_t=setTimeout(function(){C(N,M)},J.interval)}}else{A(M).unbind("mousemove",E);if(M.hoverIntent_s==1){M.hoverIntent_t=setTimeout(function(){G(N,M)},J.timeout)}}};return this.mouseover(B).mouseout(B)}})(jQuery);
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@@ -1 +1 @@
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(function($){var m={"\b":"\\b","\t":"\\t","\n":"\\n","\f":"\\f","\r":"\\r",'"':'\\"',"\\":"\\\\"},s={array:function(x){var a=["["],b,f,i,l=x.length,v;for(i=0;i<l;i+=1){v=x[i];f=s[typeof v];if(f){v=f(v);if(typeof v=="string"){if(b){a[a.length]=","}a[a.length]=v;b=true}}}a[a.length]="]";return a.join("")},"boolean":function(x){return String(x)},"null":function(x){return"null"},number:function(x){return isFinite(x)?String(x):"null"},object:function(x){if(x){if(x instanceof Array){return s.array(x)}var a=["{"],b,f,i,v;for(i in x){v=x[i];f=s[typeof v];if(f){v=f(v);if(typeof v=="string"){if(b){a[a.length]=","}a.push(s.string(i),":",v);b=true}}}a[a.length]="}";return a.join("")}return"null"},string:function(x){if(/["\\\x00-\x1f]/.test(x)){x=x.replace(/([\x00-\x1f\\"])/g,function(a,b){var c=m[b];if(c){return c}c=b.charCodeAt();return"\\u00"+Math.floor(c/16).toString(16)+(c%16).toString(16)})}return'"'+x+'"'}};$.toJSON=function(v){var f=isNaN(v)?s[typeof v]:s.number;if(f){return f(v)}};$.parseJSON=function(v,safe){if(safe===undefined){safe=$.parseJSON.safe}if(safe&&!/^("(\\.|[^"\\\n\r])*?"|[,:{}\[\]0-9.\-+Eaeflnr-u \n\r\t])+?$/.test(v)){return undefined}return eval("("+v+")")};$.parseJSON.safe=false})(jQuery);
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||||
@@ -1,7 +1,10 @@
|
||||
#!/usr/bin/env python
|
||||
"""
|
||||
usage: extract_genomic_dna.py $input $out_file1 ${input.metadata.chromCol} ${input.metadata.startCol} ${input.metadata.endCol} ${input.metadata.strandCol} $dbkey $out_format GALAXY_DATA_INDEX_DIR
|
||||
by Wen-Yu Chung
|
||||
usage: %prog $input $out_file1
|
||||
-1, --cols=N,N,N,N: Columns for start, end, strand in input file
|
||||
-d, --dbkey=N: Genome build of input file
|
||||
-o, --output_format=N: the data type of the output file
|
||||
-g, --GALAXY_DATA_INDEX_DIR=N: the directory containing alignseq.loc and twobit.loc
|
||||
"""
|
||||
from galaxy import eggs
|
||||
import pkg_resources
|
||||
@@ -10,6 +13,7 @@ import sys, string, os, re
|
||||
from bx.cookbook import doc_optparse
|
||||
import bx.seq.nib
|
||||
import bx.seq.twobit
|
||||
from galaxy.tools.util.galaxyops import *
|
||||
|
||||
assert sys.version_info[:2] >= ( 2, 4 )
|
||||
|
||||
@@ -54,32 +58,18 @@ def check_twobit_file( dbkey, GALAXY_DATA_INDEX_DIR ):
|
||||
return twobit_path
|
||||
|
||||
def __main__():
|
||||
input_filename = sys.argv[1]
|
||||
output_filename = sys.argv[2]
|
||||
includes_strand_col = False
|
||||
options, args = doc_optparse.parse( __doc__ )
|
||||
try:
|
||||
chrom_col, start_col, end_col, strand_col = parse_cols_arg( options.cols )
|
||||
dbkey = options.dbkey
|
||||
output_format = options.output_format
|
||||
GALAXY_DATA_INDEX_DIR = options.GALAXY_DATA_INDEX_DIR
|
||||
input_filename, output_filename = args
|
||||
except:
|
||||
doc_optparse.exception()
|
||||
|
||||
includes_strand_col = strand_col >= 0
|
||||
strand = None
|
||||
# If any of the following exceptions are thrown, we need to improve the metadata validator.
|
||||
try:
|
||||
chrom_col = int( sys.argv[3] ) - 1
|
||||
except:
|
||||
stop_err( "Chrom column not properly set, click the pencil icon in your history item to set it." )
|
||||
try:
|
||||
start_col = int( sys.argv[4] ) - 1
|
||||
except:
|
||||
stop_err( "Start column not properly set, click the pencil icon in your history item to set it." )
|
||||
try:
|
||||
end_col = int( sys.argv[5] ) - 1
|
||||
except:
|
||||
stop_err( "End column not properly set, click the pencil icon in your history item to set it." )
|
||||
try:
|
||||
strand_col = int( sys.argv[6] ) - 1
|
||||
if strand_col >= 0:
|
||||
includes_strand_col = True
|
||||
except:
|
||||
pass
|
||||
dbkey = sys.argv[7]
|
||||
output_format = sys.argv[8]
|
||||
GALAXY_DATA_INDEX_DIR = sys.argv[9]
|
||||
nibs = {}
|
||||
twobits = {}
|
||||
nib_path = check_nib_file( dbkey, GALAXY_DATA_INDEX_DIR )
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
<tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.1.0">
|
||||
<description>using coordinates from assembled/unassembled genomes</description>
|
||||
<command interpreter="python">extract_genomic_dna.py $input $out_file1 ${input.metadata.chromCol} ${input.metadata.startCol} ${input.metadata.endCol} ${input.metadata.strandCol} $dbkey $out_format ${GALAXY_DATA_INDEX_DIR}</command>
|
||||
<command interpreter="python">extract_genomic_dna.py $input $out_file1 -1 ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol} -d $dbkey -o $out_format -g ${GALAXY_DATA_INDEX_DIR}</command>
|
||||
<inputs>
|
||||
<param format="interval" name="input" type="data" label="Fetch sequences corresponding to Query">
|
||||
<validator type="unspecified_build" />
|
||||
|
||||
@@ -54,23 +54,22 @@ def __main__():
|
||||
|
||||
if options.chromCol: chromCol = int( options.chromCol ) - 1
|
||||
else:
|
||||
print >>sys.stderr, "Chromosome column has not been specified."
|
||||
print >>sys.stderr, "Chromosome column not set, click the pencil icon in the history item to set the metadata attributes."
|
||||
sys.exit()
|
||||
|
||||
if options.startCol: startCol = int( options.startCol ) - 1
|
||||
else:
|
||||
print >>sys.stderr, "Start column has not been specified."
|
||||
print >>sys.stderr, "Start column not set, click the pencil icon in the history item to set the metadata attributes."
|
||||
sys.exit()
|
||||
|
||||
if options.endCol: endCol = int( options.endCol ) - 1
|
||||
else:
|
||||
print >>sys.stderr, "End column has not been specified."
|
||||
print >>sys.stderr, "End column not set, click the pencil icon in the history item to set the metadata attributes."
|
||||
sys.exit()
|
||||
|
||||
if options.strandCol: strandCol = int( options.strandCol ) - 1
|
||||
else:
|
||||
print >>sys.stderr, "Strand column has not been specified."
|
||||
sys.exit()
|
||||
strandCol = -1
|
||||
|
||||
if options.interval_file: interval_file = options.interval_file
|
||||
else:
|
||||
|
||||
Reference in New Issue
Block a user