Hi - I have a tools that generates a tab-delimited text file as output. when I click the eye icon to view the data, all the fields are compressed as if there were no tabs. If I expand the history view, the little preview window shows the contents as tabbed. I've verified that the spaces are indeed '\t' tab characters. Why would Galaxy not display this file as a tab-delimited file? ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

The file is an output from a tool and in the tool's xml, its format is tabular. On Tue, Oct 27, 2015 at 3:43 AM, Björn Grüning <bjoern.gruening(a)gmail.com&gt; wrote: > Hi Ryan, > > is it recognised as 'tabular'? > > Ciao, > Bjoern > > Am 27.10.2015 um 04:42 schrieb Ryan G: > > Hi - I have a tools that generates a tab-delimited text file as output. > > when I click the eye icon to view the data, all the fields are > compressed > > as if there were no tabs. If I expand the history view, the little > preview > > window shows the contents as tabbed. I've verified that the spaces are > > indeed '\t' tab characters. Why would Galaxy not display this file as a > > tab-delimited file? > > > > > > > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

De: "Ryan G" <ngsbioinformatics(a)gmail.com&gt; À: "Carl Eberhard" <carlfeberhard(a)gmail.com&gt; Cc: &quot;&lt;galaxy-dev(a)lists.bx.psu.edu&gt;&quot; <galaxy-dev(a)lists.bx.psu.edu&gt; Envoyé: Lundi 23 Mai 2016 23:33:11 Objet: Re: [galaxy-dev] tabular file displayed without tabs

Odd because I have another tabular file that is displayed with every other line highlighted and there is not word-wrapping on the file. However the file that has the type tabular and displayed as text is word-wrapped with no lines highlighted. I suspect its not actually recognized as tabular or is being overridden where.

On Thu, Nov 12, 2015 at 10:23 AM, Carl Eberhard < carlfeberhard(a)gmail.com > wrote:

> Hi, Ryan

> Galaxy displays tabular data in the browser using a <table> tag. It *sounds > like* the behavior you see (columns losing space between one another when > narrowing the window and getting more space as you expand the window) would > reflect that.

> Carl

> On Wed, Oct 28, 2015 at 1:23 PM, Ryan G < ngsbioinformatics(a)gmail.com > > wrote:

> > The file is an output from a tool and in the tool's xml, its format is > > tabular. >

> > On Tue, Oct 27, 2015 at 3:43 AM, Björn Grüning < > > bjoern.gruening(a)gmail.com > > > > > wrote: >

> > > Hi Ryan, > > >

> > > is it recognised as 'tabular'? > > >

> > > Ciao, > > > > > > Bjoern > > >

> > > Am 27.10.2015 um 04:42 schrieb Ryan G: > > > > > > > Hi - I have a tools that generates a tab-delimited text file as > > > > output. > > > > > > > when I click the eye icon to view the data, all the fields are > > > > compressed > > > > > > > as if there were no tabs. If I expand the history view, the little > > > > preview > > > > > > > window shows the contents as tabbed. I've verified that the spaces > > > > are > > > > > > > indeed '\t' tab characters. Why would Galaxy not display this file as > > > > a > > > > > > > tab-delimited file? > > > > > > > > > > > > > > > > > > > > > > > > > > > > ___________________________________________________________ > > > > > > > Please keep all replies on the list by using "reply all" > > > > > > > in your mail client. To manage your subscriptions to this > > > > > > > and other Galaxy lists, please use the interface at: > > > > > > > https://lists.galaxyproject.org/ > > > > > > > > > > > > > > To search Galaxy mailing lists use the unified search at: > > > > > > > http://galaxyproject.org/search/mailinglists/ > > > > > > > > > >

> > ___________________________________________________________ > > > Please keep all replies on the list by using "reply all" > > > in your mail client. To manage your subscriptions to this > > > and other Galaxy lists, please use the interface at: > > > https://lists.galaxyproject.org/ >

> > To search Galaxy mailing lists use the unified search at: > > > http://galaxyproject.org/search/mailinglists/ >

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

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Ok - if it's not zebra striped and it's word wrapping, then it's somehow not displaying as tabular - you're correct. If you click on the 'View details' button of that dataset (the 'i' with the circle around it shown when the dataset is expanded in the right hand side of the 'Analyze Data' page), what does it list the 'Format' as? 'tabular'? (This is also listed as 'Format' in the expanded view itself). On Mon, May 23, 2016 at 5:33 PM, Ryan G <ngsbioinformatics(a)gmail.com&gt; wrote: > Odd because I have another tabular file that is displayed with every > other line highlighted and there is not word-wrapping on the file. However > the file that has the type tabular and displayed as text is word-wrapped > with no lines highlighted. I suspect its not actually recognized as > tabular or is being overridden where. > > > On Thu, Nov 12, 2015 at 10:23 AM, Carl Eberhard <carlfeberhard(a)gmail.com&gt; > wrote: > >> Hi, Ryan >> >> Galaxy displays tabular data in the browser using a <table> tag. It >> *sounds like* the behavior you see (columns losing space between one >> another when narrowing the window and getting more space as you expand the >> window) would reflect that. >> >> Carl >> >> On Wed, Oct 28, 2015 at 1:23 PM, Ryan G <ngsbioinformatics(a)gmail.com&gt; >> wrote: >> >>> The file is an output from a tool and in the tool's xml, its format is >>> tabular. >>> >>> >>> >>> On Tue, Oct 27, 2015 at 3:43 AM, Björn Grüning < >>> bjoern.gruening(a)gmail.com&gt; wrote: >>> >>>> Hi Ryan, >>>> >>>> is it recognised as 'tabular'? >>>> >>>> Ciao, >>>> Bjoern >>>> >>>> Am 27.10.2015 um 04:42 schrieb Ryan G: >>>> > Hi - I have a tools that generates a tab-delimited text file as >>>> output. >>>> > when I click the eye icon to view the data, all the fields are >>>> compressed >>>> > as if there were no tabs. If I expand the history view, the little >>>> preview >>>> > window shows the contents as tabbed. I've verified that the spaces >>>> are >>>> > indeed '\t' tab characters. Why would Galaxy not display this file >>>> as a >>>> > tab-delimited file? >>>> > >>>> > >>>> > >>>> > ___________________________________________________________ >>>> > Please keep all replies on the list by using "reply all" >>>> > in your mail client. To manage your subscriptions to this >>>> > and other Galaxy lists, please use the interface at: >>>> > https://lists.galaxyproject.org/ >>>> > >>>> > To search Galaxy mailing lists use the unified search at: >>>> > http://galaxyproject.org/search/mailinglists/ >>>> > >>>> >>> >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> https://lists.galaxyproject.org/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >> >> >

Strange. Alright, a few questions then: * Is this the only file that this happens to? Do other outputs from this tool produce the same sort of error? * Do you see any javascript errors in the console when attempting the viewing? (how to here: http://webmasters.stackexchange.com/a/77337) On Fri, May 27, 2016 at 12:42 PM, Ryan G <ngsbioinformatics(a)gmail.com&gt; wrote: > The format is listed as tabular when I view details. > > In fact, in the preview window in the History Pane, it recognizes there > are columns and that the data is in fact tabular, but when displaying, this > isn't the case. > > > > On Tue, May 24, 2016 at 4:20 PM, Carl Eberhard <carlfeberhard(a)gmail.com&gt; > wrote: > >> Ok - if it's not zebra striped and it's word wrapping, then it's somehow >> not displaying as tabular - you're correct. >> >> If you click on the 'View details' button of that dataset (the 'i' with >> the circle around it shown when the dataset is expanded in the right hand >> side of the 'Analyze Data' page), what does it list the 'Format' as? >> 'tabular'? (This is also listed as 'Format' in the expanded view itself). >> >> On Mon, May 23, 2016 at 5:33 PM, Ryan G <ngsbioinformatics(a)gmail.com&gt; >> wrote: >> >>> Odd because I have another tabular file that is displayed with every >>> other line highlighted and there is not word-wrapping on the file. However >>> the file that has the type tabular and displayed as text is word-wrapped >>> with no lines highlighted. I suspect its not actually recognized as >>> tabular or is being overridden where. >>> >>> >>> On Thu, Nov 12, 2015 at 10:23 AM, Carl Eberhard < >>> carlfeberhard(a)gmail.com&gt; wrote: >>> >>>> Hi, Ryan >>>> >>>> Galaxy displays tabular data in the browser using a <table> tag. It >>>> *sounds like* the behavior you see (columns losing space between one >>>> another when narrowing the window and getting more space as you expand the >>>> window) would reflect that. >>>> >>>> Carl >>>> >>>> On Wed, Oct 28, 2015 at 1:23 PM, Ryan G <ngsbioinformatics(a)gmail.com&gt; >>>> wrote: >>>> >>>>> The file is an output from a tool and in the tool's xml, its format >>>>> is tabular. >>>>> >>>>> >>>>> >>>>> On Tue, Oct 27, 2015 at 3:43 AM, Björn Grüning < >>>>> bjoern.gruening(a)gmail.com&gt; wrote: >>>>> >>>>>> Hi Ryan, >>>>>> >>>>>> is it recognised as 'tabular'? >>>>>> >>>>>> Ciao, >>>>>> Bjoern >>>>>> >>>>>> Am 27.10.2015 um 04:42 schrieb Ryan G: >>>>>> > Hi - I have a tools that generates a tab-delimited text file as >>>>>> output. >>>>>> > when I click the eye icon to view the data, all the fields are >>>>>> compressed >>>>>> > as if there were no tabs. If I expand the history view, the >>>>>> little preview >>>>>> > window shows the contents as tabbed. I've verified that the >>>>>> spaces are >>>>>> > indeed '\t' tab characters. Why would Galaxy not display this >>>>>> file as a >>>>>> > tab-delimited file? >>>>>> > >>>>>> > >>>>>> > >>>>>> > ___________________________________________________________ >>>>>> > Please keep all replies on the list by using "reply all" >>>>>> > in your mail client. To manage your subscriptions to this >>>>>> > and other Galaxy lists, please use the interface at: >>>>>> > https://lists.galaxyproject.org/ >>>>>> > >>>>>> > To search Galaxy mailing lists use the unified search at: >>>>>> > http://galaxyproject.org/search/mailinglists/ >>>>>> > >>>>>> >>>>> >>>>> >>>>> ___________________________________________________________ >>>>> Please keep all replies on the list by using "reply all" >>>>> in your mail client. To manage your subscriptions to this >>>>> and other Galaxy lists, please use the interface at: >>>>> https://lists.galaxyproject.org/ >>>>> >>>>> To search Galaxy mailing lists use the unified search at: >>>>> http://galaxyproject.org/search/mailinglists/ >>>>> >>>> >>>> >>> >> > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

No, it happens to all output from this particular tool. I do see a javascript warning in the console, 'The character encoding of a framed document was not declared. The document may appear different if view without the document framing it.' The file does have 64 columns in it. Is there a way to change Galaxy's default from 50 to something more? On Tue, May 31, 2016 at 8:17 AM, Carl Eberhard <carlfeberhard(a)gmail.com&gt; wrote: > Strange. Alright, a few questions then: > > * Is this the only file that this happens to? Do other outputs from this > tool produce the same sort of error? > * Do you see any javascript errors in the console when attempting the > viewing? (how to here: http://webmasters.stackexchange.com/a/77337) > > On Fri, May 27, 2016 at 12:42 PM, Ryan G <ngsbioinformatics(a)gmail.com&gt; > wrote: > >> The format is listed as tabular when I view details. >> >> In fact, in the preview window in the History Pane, it recognizes there >> are columns and that the data is in fact tabular, but when displaying, this >> isn't the case. >> >> >> >> On Tue, May 24, 2016 at 4:20 PM, Carl Eberhard <carlfeberhard(a)gmail.com&gt; >> wrote: >> >>> Ok - if it's not zebra striped and it's word wrapping, then it's >>> somehow not displaying as tabular - you're correct. >>> >>> If you click on the 'View details' button of that dataset (the 'i' with >>> the circle around it shown when the dataset is expanded in the right hand >>> side of the 'Analyze Data' page), what does it list the 'Format' as? >>> 'tabular'? (This is also listed as 'Format' in the expanded view itself). >>> >>> On Mon, May 23, 2016 at 5:33 PM, Ryan G <ngsbioinformatics(a)gmail.com&gt; >>> wrote: >>> >>>> Odd because I have another tabular file that is displayed with every >>>> other line highlighted and there is not word-wrapping on the file. However >>>> the file that has the type tabular and displayed as text is word-wrapped >>>> with no lines highlighted. I suspect its not actually recognized as >>>> tabular or is being overridden where. >>>> >>>> >>>> On Thu, Nov 12, 2015 at 10:23 AM, Carl Eberhard < >>>> carlfeberhard(a)gmail.com&gt; wrote: >>>> >>>>> Hi, Ryan >>>>> >>>>> Galaxy displays tabular data in the browser using a <table> tag. It >>>>> *sounds like* the behavior you see (columns losing space between one >>>>> another when narrowing the window and getting more space as you expand the >>>>> window) would reflect that. >>>>> >>>>> Carl >>>>> >>>>> On Wed, Oct 28, 2015 at 1:23 PM, Ryan G <ngsbioinformatics(a)gmail.com&gt; >>>>> wrote: >>>>> >>>>>> The file is an output from a tool and in the tool's xml, its format >>>>>> is tabular. >>>>>> >>>>>> >>>>>> >>>>>> On Tue, Oct 27, 2015 at 3:43 AM, Björn Grüning < >>>>>> bjoern.gruening(a)gmail.com&gt; wrote: >>>>>> >>>>>>> Hi Ryan, >>>>>>> >>>>>>> is it recognised as 'tabular'? >>>>>>> >>>>>>> Ciao, >>>>>>> Bjoern >>>>>>> >>>>>>> Am 27.10.2015 um 04:42 schrieb Ryan G: >>>>>>> > Hi - I have a tools that generates a tab-delimited text file as >>>>>>> output. >>>>>>> > when I click the eye icon to view the data, all the fields are >>>>>>> compressed >>>>>>> > as if there were no tabs. If I expand the history view, the >>>>>>> little preview >>>>>>> > window shows the contents as tabbed. I've verified that the >>>>>>> spaces are >>>>>>> > indeed '\t' tab characters. Why would Galaxy not display this >>>>>>> file as a >>>>>>> > tab-delimited file? >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> > ___________________________________________________________ >>>>>>> > Please keep all replies on the list by using "reply all" >>>>>>> > in your mail client. To manage your subscriptions to this >>>>>>> > and other Galaxy lists, please use the interface at: >>>>>>> > https://lists.galaxyproject.org/ >>>>>>> > >>>>>>> > To search Galaxy mailing lists use the unified search at: >>>>>>> > http://galaxyproject.org/search/mailinglists/ >>>>>>> > >>>>>>> >>>>>> >>>>>> >>>>>> ___________________________________________________________ >>>>>> Please keep all replies on the list by using "reply all" >>>>>> in your mail client. To manage your subscriptions to this >>>>>> and other Galaxy lists, please use the interface at: >>>>>> https://lists.galaxyproject.org/ >>>>>> >>>>>> To search Galaxy mailing lists use the unified search at: >>>>>> http://galaxyproject.org/search/mailinglists/ >>>>>> >>>>> >>>>> >>>> >>> >> > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

That fixes it. Thanks! On Tue, Jun 14, 2016 at 10:33 AM, Dannon Baker <dannon.baker(a)gmail.com&gt; wrote: > Ok, so it's definitely the column limit that's causing the unexpected > style-less display. This currently isn't configurable per-galaxy (the plan > was to add more appropriate displays for many-columned files), but here's a > quick gist to show you how you might tweak this locally: > > https://gist.github.com/dannon/f67cccd16f9e8c8776a0032b11d1c5c7 > > This would be really easy to turn into an app configuration setting in > galaxy.ini if it seems like something folks would want though I opted not > to do so originally to avoid configuration bloat for what seemed like a > very niche case. > > On Tue, Jun 14, 2016 at 10:23 AM Ryan G <ngsbioinformatics(a)gmail.com&gt; > wrote: > >> No, it happens to all output from this particular tool. >> >> I do see a javascript warning in the console, 'The character encoding of >> a framed document was not declared. The document may appear different if >> view without the document framing it.' >> >> The file does have 64 columns in it. Is there a way to change Galaxy's >> default from 50 to something more? >> >> >> >> On Tue, May 31, 2016 at 8:17 AM, Carl Eberhard <carlfeberhard(a)gmail.com&gt; >> wrote: >> >>> Strange. Alright, a few questions then: >>> >>> * Is this the only file that this happens to? Do other outputs from >>> this tool produce the same sort of error? >>> * Do you see any javascript errors in the console when attempting the >>> viewing? (how to here: http://webmasters.stackexchange.com/a/77337) >>> >>> On Fri, May 27, 2016 at 12:42 PM, Ryan G <ngsbioinformatics(a)gmail.com&gt; >>> wrote: >>> >>>> The format is listed as tabular when I view details. >>>> >>>> In fact, in the preview window in the History Pane, it recognizes >>>> there are columns and that the data is in fact tabular, but when >>>> displaying, this isn't the case. >>>> >>>> >>>> >>>> On Tue, May 24, 2016 at 4:20 PM, Carl Eberhard < >>>> carlfeberhard(a)gmail.com&gt; wrote: >>>> >>>>> Ok - if it's not zebra striped and it's word wrapping, then it's >>>>> somehow not displaying as tabular - you're correct. >>>>> >>>>> If you click on the 'View details' button of that dataset (the 'i' >>>>> with the circle around it shown when the dataset is expanded in the right >>>>> hand side of the 'Analyze Data' page), what does it list the 'Format' as? >>>>> 'tabular'? (This is also listed as 'Format' in the expanded view itself). >>>>> >>>>> On Mon, May 23, 2016 at 5:33 PM, Ryan G <ngsbioinformatics(a)gmail.com&gt; >>>>> wrote: >>>>> >>>>>> Odd because I have another tabular file that is displayed with every >>>>>> other line highlighted and there is not word-wrapping on the file. However >>>>>> the file that has the type tabular and displayed as text is word-wrapped >>>>>> with no lines highlighted. I suspect its not actually recognized as >>>>>> tabular or is being overridden where. >>>>>> >>>>>> >>>>>> On Thu, Nov 12, 2015 at 10:23 AM, Carl Eberhard < >>>>>> carlfeberhard(a)gmail.com&gt; wrote: >>>>>> >>>>>>> Hi, Ryan >>>>>>> >>>>>>> Galaxy displays tabular data in the browser using a <table> tag. It >>>>>>> *sounds like* the behavior you see (columns losing space between one >>>>>>> another when narrowing the window and getting more space as you expand the >>>>>>> window) would reflect that. >>>>>>> >>>>>>> Carl >>>>>>> >>>>>>> On Wed, Oct 28, 2015 at 1:23 PM, Ryan G < >>>>>>> ngsbioinformatics(a)gmail.com&gt; wrote: >>>>>>> >>>>>>>> The file is an output from a tool and in the tool's xml, its >>>>>>>> format is tabular. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Tue, Oct 27, 2015 at 3:43 AM, Björn Grüning < >>>>>>>> bjoern.gruening(a)gmail.com&gt; wrote: >>>>>>>> >>>>>>>>> Hi Ryan, >>>>>>>>> >>>>>>>>> is it recognised as 'tabular'? >>>>>>>>> >>>>>>>>> Ciao, >>>>>>>>> Bjoern >>>>>>>>> >>>>>>>>> Am 27.10.2015 um 04:42 schrieb Ryan G: >>>>>>>>> > Hi - I have a tools that generates a tab-delimited text file as >>>>>>>>> output. >>>>>>>>> > when I click the eye icon to view the data, all the fields are >>>>>>>>> compressed >>>>>>>>> > as if there were no tabs. If I expand the history view, the >>>>>>>>> little preview >>>>>>>>> > window shows the contents as tabbed. I've verified that the >>>>>>>>> spaces are >>>>>>>>> > indeed '\t' tab characters. Why would Galaxy not display this >>>>>>>>> file as a >>>>>>>>> > tab-delimited file? >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> > ___________________________________________________________ >>>>>>>>> > Please keep all replies on the list by using "reply all" >>>>>>>>> > in your mail client. To manage your subscriptions to this >>>>>>>>> > and other Galaxy lists, please use the interface at: >>>>>>>>> > https://lists.galaxyproject.org/ >>>>>>>>> > >>>>>>>>> > To search Galaxy mailing lists use the unified search at: >>>>>>>>> > http://galaxyproject.org/search/mailinglists/ >>>>>>>>> > >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ___________________________________________________________ >>>>>>>> Please keep all replies on the list by using "reply all" >>>>>>>> in your mail client. To manage your subscriptions to this >>>>>>>> and other Galaxy lists, please use the interface at: >>>>>>>> https://lists.galaxyproject.org/ >>>>>>>> >>>>>>>> To search Galaxy mailing lists use the unified search at: >>>>>>>> http://galaxyproject.org/search/mailinglists/ >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > >