Adding a tool with additional html/js interface to make input selection
Hi, We are trying to add a new tool to our local galaxy instance with the following requirements. When a user clicks on the tool in side panel from tools list, a table display should appear where the first element in each row is a clickable link. Users can click on any of the element, and then see only there selected row and another table with more options. Once user has made all the selections, then a form should appear describing that you have made the following selection, do you want to execute the tool now? And then users can submit the job. If we implement such a thing in galaxy, we need to load a page with aforementioned functionality, then map the users selection to the tool's inputs, and then run the tool. The question is, is there a way in galaxy to load an html with javascript and use it to prepare the inputs for the tool we want to run, using the xml wrapper. Thanks, Saba
Hi, We are trying to add a new tool to our local galaxy instance with the following requirements. When a user clicks on the tool in side panel from tools list, a table should appear where the first element in each row is a clickable link. Users can click on any of the element, and then see only there selected row and another table with more options. Once user has made all the selections, then a form should appear describing that user has made the following selection, if he/she wishes to execute the tool now? And then users can submit the job. If we implement such a thing in galaxy, we need to load a page with aforementioned functionality, then map the users selection to the tool's inputs, and then run the application i.e. the command line to execute it. Is there a way in galaxy to load an html with javascript and use it to prepare the inputs for the application we want to run, using the xml tool wrapper. Thanks, Saba
On Tue, Feb 18, 2014 at 5:19 PM, Saba Sehrish <ssehrish@fnal.gov> wrote:
Hi,
We are trying to add a new tool to our local galaxy instance with the following requirements.
When a user clicks on the tool in side panel from tools list, a table should appear where the first element in each row is a clickable link. Users can click on any of the element, and then see only there selected row and another table with more options. Once user has made all the selections, then a form should appear describing that user has made the following selection, if he/she wishes to execute the tool now? And then users can submit the job.
If we implement such a thing in galaxy, we need to load a page with aforementioned functionality, then map the users selection to the tool's inputs, and then run the application i.e. the command line to execute it. Is there a way in galaxy to load an html with javascript and use it to prepare the inputs for the application we want to run, using the xml tool wrapper.
Thanks, Saba
Might selections from static tables defined in *.loc files work, coupled to some conditionals so the second table changes? Peter
I am using *.loc files, to create a bunch of tables I need, but I want to display complete tables (e.g. from .loc file) with clickable elements for users so that their input could be captured. For example if in my .loc file I have the following contents Model Size Path M001 L180 full path to some file M002 L256 full path to some file … And I want this information to appear in the form of an html table (can be some other table as well) when user loads the tool, and all M001, M002 should be clickable elements. Once clicked they should be navigated to another table with more options. On Feb 18, 2014, at 11:37 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Tue, Feb 18, 2014 at 5:19 PM, Saba Sehrish <ssehrish@fnal.gov> wrote:
Hi,
We are trying to add a new tool to our local galaxy instance with the following requirements.
When a user clicks on the tool in side panel from tools list, a table should appear where the first element in each row is a clickable link. Users can click on any of the element, and then see only there selected row and another table with more options. Once user has made all the selections, then a form should appear describing that user has made the following selection, if he/she wishes to execute the tool now? And then users can submit the job.
If we implement such a thing in galaxy, we need to load a page with aforementioned functionality, then map the users selection to the tool's inputs, and then run the application i.e. the command line to execute it. Is there a way in galaxy to load an html with javascript and use it to prepare the inputs for the application we want to run, using the xml tool wrapper.
Thanks, Saba
Might selections from static tables defined in *.loc files work, coupled to some conditionals so the second table changes?
Peter
On Tue, Feb 18, 2014 at 6:14 PM, Saba Sehrish <ssehrish@fnal.gov> wrote:
I am using *.loc files, to create a bunch of tables I need, but I want to display complete tables (e.g. from .loc file) with clickable elements for users so that their input could be captured.
For example if in my .loc file I have the following contents
Model Size Path M001 L180 full path to some file M002 L256 full path to some file ...
And I want this information to appear in the form of an html table (can be some other table as well) when user loads the tool, and all M001, M002 should be clickable elements.
Once clicked they should be navigated to another table with more options.
By clickable, are you wanting selection by row - or by cell? If by row this doesn't sound so different to how Galaxy's current *.loc parameters work... Peter
On Feb 18, 2014, at 12:23 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Tue, Feb 18, 2014 at 6:14 PM, Saba Sehrish <ssehrish@fnal.gov> wrote:
I am using *.loc files, to create a bunch of tables I need, but I want to display complete tables (e.g. from .loc file) with clickable elements for users so that their input could be captured.
For example if in my .loc file I have the following contents
Model Size Path M001 L180 full path to some file M002 L256 full path to some file ...
And I want this information to appear in the form of an html table (can be some other table as well) when user loads the tool, and all M001, M002 should be clickable elements.
Once clicked they should be navigated to another table with more options.
By clickable, are you wanting selection by row - or by cell? If by row this doesn't sound so different to how Galaxy's current *.loc parameters work...
Peter
Its a row but the concern is that each row has 10 numbers in it, and I have tried using .loc file to display this information to the users in the form of a pull-down menu. It is difficult for users to see the complete row with proper formatting and table header to describe what does each number mean. So the idea is to display this information in the form of a table (using html, js) to the users instead of a select/pull down menu.
On Tue, Feb 18, 2014 at 7:13 PM, Saba Sehrish <ssehrish@fnal.gov> wrote:
On Feb 18, 2014, at 12:23 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
I am using *.loc files, to create a bunch of tables I need, but I want to display complete tables (e.g. from .loc file) with clickable elements for users so that their input could be captured.
For example if in my .loc file I have the following contents
Model Size Path M001 L180 full path to some file M002 L256 full path to some file ...
And I want this information to appear in the form of an html table (can be some other table as well) when user loads the tool, and all M001, M002 should be clickable elements.
Once clicked they should be navigated to another table with more
On Tue, Feb 18, 2014 at 6:14 PM, Saba Sehrish <ssehrish@fnal.gov> wrote: options.
By clickable, are you wanting selection by row - or by cell? If by row this doesn't sound so different to how Galaxy's current *.loc parameters work...
Peter
Its a row but the concern is that each row has 10 numbers in
it, and I have tried using .loc file to display this information to the users in the form of a pull-down menu. It is difficult for users to see the complete row with proper formatting and table header to describe what does each number mean. So the idea is to display this information in the form of a table (using html, js) to the users instead of a select/pull down menu.
OK - so no deep changes to the Galaxy parameter data model etc would be needed (which is good news), 'just' a new table rendering of a *.loc based parameter. However, I'm not in a position to judge how much work that would be... On the bright side, from the API and functional testing point of view, this would be just like the current *.loc based parameters (Hopefully one of the Galaxy team can give you a more informed opinion.) Peter
On Feb 18, 2014, at 3:22 PM, Peter Cock <p.j.a.cock@googlemail.com<mailto:p.j.a.cock@googlemail.com>> wrote: On Tue, Feb 18, 2014 at 7:13 PM, Saba Sehrish <ssehrish@fnal.gov<mailto:ssehrish@fnal.gov>> wrote: On Feb 18, 2014, at 12:23 PM, Peter Cock <p.j.a.cock@googlemail.com<mailto:p.j.a.cock@googlemail.com>> wrote:
On Tue, Feb 18, 2014 at 6:14 PM, Saba Sehrish <ssehrish@fnal.gov<mailto:ssehrish@fnal.gov>> wrote:
I am using *.loc files, to create a bunch of tables I need, but I want to display complete tables (e.g. from .loc file) with clickable elements for users so that their input could be captured.
For example if in my .loc file I have the following contents
Model Size Path M001 L180 full path to some file M002 L256 full path to some file ...
And I want this information to appear in the form of an html table (can be some other table as well) when user loads the tool, and all M001, M002 should be clickable elements.
Once clicked they should be navigated to another table with more options.
By clickable, are you wanting selection by row - or by cell? If by row this doesn't sound so different to how Galaxy's current *.loc parameters work...
Peter
Its a row but the concern is that each row has 10 numbers in it, and I have tried using .loc file to display this information to the users in the form of a pull-down menu. It is difficult for users to see the complete row with proper formatting and table header to describe what does each number mean. So the idea is to display this information in the form of a table (using html, js) to the users instead of a select/pull down menu. OK - so no deep changes to the Galaxy parameter data model etc would be needed (which is good news), 'just' a new table rendering of a *.loc based parameter. However, I'm not in a position to judge how much work that would be… Yes, correct. Thats the part where I am stuck. all the galaxy tools are expected to work from command line, but here we need to extract the inputs from a ”rendered table” out of .loc file. I have tried to embed some html in the wrapper xml file for the tool, I am using CDATA and then html tags with in it and combine with xml input tags for the command line but it still does’t get me closer to what I need to do. On the bright side, from the API and functional testing point of view, this would be just like the current *.loc based parameters (Hopefully one of the Galaxy team can give you a more informed opinion.) Peter
On Tue, Feb 18, 2014 at 9:59 PM, Saba Sehrish <ssehrish@fnal.gov> wrote:
On Feb 18, 2014, at 3:22 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
OK - so no deep changes to the Galaxy parameter data model etc would be needed (which is good news), 'just' a new table rendering of a *.loc based parameter. However, I'm not in a position to judge how much work that would be...
Yes, correct. Thats the part where I am stuck. all the galaxy tools are expected to work from command line, but here we need to extract the inputs from a "rendered table" out of .loc file. I have tried to embed some html in the wrapper xml file for the tool, I am using CDATA and then html tags with in it and combine with xml input tags for the command line but it still does't get me closer to what I need to do.
I very much doubt this could be done in an individual tool wrapper XML file. Unless there is some trick I'm missing, in order to do this you (or someone else) will have to add new code to the Galaxy core itself. Essentially, in addition to the current *.loc based <param> display options like drop down selection lists, and multi- select check boxes, a new table based view would be needed. But as I said, a more expert opinion from the Galaxy team would be useful here. Peter
On Feb 18, 2014, at 4:09 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Tue, Feb 18, 2014 at 9:59 PM, Saba Sehrish <ssehrish@fnal.gov> wrote:
On Feb 18, 2014, at 3:22 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
OK - so no deep changes to the Galaxy parameter data model etc would be needed (which is good news), 'just' a new table rendering of a *.loc based parameter. However, I'm not in a position to judge how much work that would be...
Yes, correct. Thats the part where I am stuck. all the galaxy tools are expected to work from command line, but here we need to extract the inputs from a "rendered table" out of .loc file. I have tried to embed some html in the wrapper xml file for the tool, I am using CDATA and then html tags with in it and combine with xml input tags for the command line but it still does't get me closer to what I need to do.
I very much doubt this could be done in an individual tool wrapper XML file. Unless there is some trick I'm missing, in order to do this you (or someone else) will have to add new code to the Galaxy core itself.
Essentially, in addition to the current *.loc based <param> display options like drop down selection lists, and multi- select check boxes, a new table based view would be needed.
But as I said, a more expert opinion from the Galaxy team would be useful here.
Peter
I agree to what you said based on my limited experience and exploring of galaxy. Lets wait and see what Galaxy team’s opinion is.
Hi all, I am trying to write a tool that based on user criteria will run a different script. In the code below, If I select Use_Snapshot, I see the right interface but somehow galaxy tries to execute the #else part and look for “m” input parameter. The example I have seen in documentation is using the script with same name in both if and else and the number of input arguments is the same as well. Any suggestions/ideas why always #else part gets executed although right interface appears based on user selection. Thanks, Saba <command> #if $source.source_select==“Use_Snapshot" cM-snapshot.sh $input $output #else cM.sh $m $b $ns $w $s $z $output #end if </command> <inputs> <conditional name="source"> <param name="source_select" type="select" label="Specify the input"> <option value="Use_Snapshot">Use Snapshot</option> <option value="Set_Values">Set Values</option> </param> <when value="Use_Snapshot"> <param name="input" type="data" format="dbm" size="100" label="Input Snapshot"/> <sanitizer sanitize="False"/> </when> <when value="Set_Values"> <param name="m" label="Omega_m h^2" type="float" value="0.1279" min="0.120" max="0.155"/> <param name="b" label="Omega_b h^2" type="float" value="0.0232" min="0.0215" max="0.0235"/> <param name="ns" label="n_s" type="float" value="0.8629" min="0.85" max="1.05"/> <param name="w" label="w" type="float" value="-1.184" min="-1.30" max="-0.70"/> <param name="s" label="sigma_8" type="float" value="0.6159" min="0.61" max="0.9"/> <param name="z" label="z" type="float" value="1.0" min="0.0" max="1.0"/> <sanitizer sanitize="False"/> </when> </conditional> </inputs>
Hi Saba, there is a syntax error in the line of the "#if". Please add ":" at the end and report whether the error still occurs. All the best, Jens Von: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Im Auftrag von Saba Sehrish Gesendet: Mittwoch, 19. März 2014 23:07 An: galaxy-dev@lists.bx.psu.edu Betreff: [galaxy-dev] Running a different command based on selection in the tool Hi all, I am trying to write a tool that based on user criteria will run a different script. In the code below, If I select Use_Snapshot, I see the right interface but somehow galaxy tries to execute the #else part and look for "m" input parameter. The example I have seen in documentation is using the script with same name in both if and else and the number of input arguments is the same as well. Any suggestions/ideas why always #else part gets executed although right interface appears based on user selection. Thanks, Saba <command> #if $source.source_select=="Use_Snapshot" cM-snapshot.sh $input $output #else cM.sh $m $b $ns $w $s $z $output #end if </command> <inputs> <conditional name="source"> <param name="source_select" type="select" label="Specify the input"> <option value="Use_Snapshot">Use Snapshot</option> <option value="Set_Values">Set Values</option> </param> <when value="Use_Snapshot"> <param name="input" type="data" format="dbm" size="100" label="Input Snapshot"/> <sanitizer sanitize="False"/> </when> <when value="Set_Values"> <param name="m" label="Omega_m h^2" type="float" value="0.1279" min="0.120" max="0.155"/> <param name="b" label="Omega_b h^2" type="float" value="0.0232" min="0.0215" max="0.0235"/> <param name="ns" label="n_s" type="float" value="0.8629" min="0.85" max="1.05"/> <param name="w" label="w" type="float" value="-1.184" min="-1.30" max="-0.70"/> <param name="s" label="sigma_8" type="float" value="0.6159" min="0.61" max="0.9"/> <param name="z" label="z" type="float" value="1.0" min="0.0" max="1.0"/> <sanitizer sanitize="False"/> </when> </conditional> </inputs>
Hi Saba and Jens, ":" are not needed, they are optional, see http://www.cheetahtemplate.org/docs/users_guide_html/users_guide.html#SECTIO... Maybe it's a problem with the left quotes around Use_Snapshot in the #if line? Nicola Il 2014-03-20 06:26 Keilwagen, Jens ha scritto:
Hi Saba,
there is a syntax error in the line of the "#if". Please add ":" at the end and report whether the error still occurs.
All the best, Jens
VON: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] IM AUFTRAG VON Saba Sehrish GESENDET: Mittwoch, 19. März 2014 23:07 AN: galaxy-dev@lists.bx.psu.edu BETREFF: [galaxy-dev] Running a different command based on selection in the tool
Hi all,
I am trying to write a tool that based on user criteria will run a different script.
In the code below, If I select Use_Snapshot, I see the right interface but somehow galaxy tries to execute the #else part and look for "m" input parameter. The example I have seen in documentation is using the script with same name in both if and else and the number of input arguments is the same as well. Any suggestions/ideas why always #else part gets executed although right interface appears based on user selection.
Thanks,
Saba
<command>
#if $source.source_select=="Use_Snapshot"
cM-snapshot.sh $input $output
#else
cM.sh $m $b $ns $w $s $z $output
#end if
</command>
<inputs>
<conditional name="source">
<param name="source_select" type="select" label="Specify the input">
<option value="Use_Snapshot">Use Snapshot</option>
<option value="Set_Values">Set Values</option>
</param>
<when value="Use_Snapshot">
<param name="input" type="data" format="dbm" size="100" label="Input Snapshot"/>
<sanitizer sanitize="False"/>
</when>
<when value="Set_Values">
<param name="m" label="Omega_m h^2" type="float" value="0.1279" min="0.120" max="0.155"/>
<param name="b" label="Omega_b h^2" type="float" value="0.0232" min="0.0215" max="0.0235"/>
<param name="ns" label="n_s" type="float" value="0.8629" min="0.85" max="1.05"/>
<param name="w" label="w" type="float" value="-1.184" min="-1.30" max="-0.70"/>
<param name="s" label="sigma_8" type="float" value="0.6159" min="0.61" max="0.9"/>
<param name="z" label="z" type="float" value="1.0" min="0.0" max="1.0"/>
<sanitizer sanitize="False"/>
</when>
</conditional>
</inputs>
Hi all, It may be the comparison, I've sometimes found an explicit cast to str is required in this kind of situation. So, I would try: <command> #if str($source.source_select)=="Use_Snapshot": cM-snapshot.sh $input $output #else cM.sh $m $b $ns $w $s $z $output #end if </command> Regards, Peter On Thu, Mar 20, 2014 at 10:17 AM, Nicola Soranzo <soranzo@crs4.it> wrote:
Hi Saba and Jens, ":" are not needed, they are optional, see
http://www.cheetahtemplate.org/docs/users_guide_html/users_guide.html#SECTIO...
Maybe it's a problem with the left quotes around Use_Snapshot in the #if line?
Nicola
Il 2014-03-20 06:26 Keilwagen, Jens ha scritto:
Hi Saba,
there is a syntax error in the line of the "#if". Please add ":" at the end and report whether the error still occurs.
All the best, Jens
VON: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] IM AUFTRAG VON Saba Sehrish GESENDET: Mittwoch, 19. März 2014 23:07 AN: galaxy-dev@lists.bx.psu.edu BETREFF: [galaxy-dev] Running a different command based on selection
in the tool
Hi all,
I am trying to write a tool that based on user criteria will run a different script.
In the code below, If I select Use_Snapshot, I see the right interface but somehow galaxy tries to execute the #else part and look for "m" input parameter. The example I have seen in documentation is using the script with same name in both if and else and the number of input arguments is the same as well. Any suggestions/ideas why always #else part gets executed although right interface appears based on user selection.
Thanks,
Saba
<command>
#if $source.source_select=="Use_Snapshot"
cM-snapshot.sh $input $output
#else
cM.sh $m $b $ns $w $s $z $output
#end if
</command>
<inputs>
<conditional name="source">
<param name="source_select" type="select" label="Specify the input">
<option value="Use_Snapshot">Use Snapshot</option>
<option value="Set_Values">Set Values</option>
</param>
<when value="Use_Snapshot">
<param name="input" type="data" format="dbm" size="100" label="Input Snapshot"/>
<sanitizer sanitize="False"/>
</when>
<when value="Set_Values">
<param name="m" label="Omega_m h^2" type="float" value="0.1279" min="0.120" max="0.155"/>
<param name="b" label="Omega_b h^2" type="float" value="0.0232" min="0.0215" max="0.0235"/>
<param name="ns" label="n_s" type="float" value="0.8629" min="0.85" max="1.05"/>
<param name="w" label="w" type="float" value="-1.184" min="-1.30" max="-0.70"/>
<param name="s" label="sigma_8" type="float" value="0.6159" min="0.61" max="0.9"/>
<param name="z" label="z" type="float" value="1.0" min="0.0" max="1.0"/>
<sanitizer sanitize="False"/>
</when>
</conditional>
</inputs>
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Hi all, For all the input parameters, we have to explicitly use $source.input, $source.m, etc instead of just using input, m, etc. Please see the code below that works. <command> #if $source.source_select=="Use_Snapshot" ./cM-snapshot.sh $source.input $output #else ./cM.sh $source.m $source.b $source.ns $source.w $source.s $source.z $output #end if </command> <inputs> <conditional name="source"> <param name="source_select" type="select" label="Specify the input"> <option value="Use_Snapshot">Use Snapshot</option> <option value="Set_Values">Set Values</option> </param> <when value="Use_Snapshot"> <param name="input" type="data" format="dbm" size="100" label="Input Snapshot"/> <sanitizer sanitize="False"/> </when> <when value="Set_Values"> <param name="m" label="Omega_m h^2" type="float" value="0.1279" min="0.120" max="0.155"/> <param name="b" label="Omega_b h^2" type="float" value="0.0232" min="0.0215" max="0.0235"/> <param name="ns" label="n_s" type="float" value="0.8629" min="0.85" max="1.05"/> <param name="w" label="w" type="float" value="-1.184" min="-1.30" max="-0.70"/> <param name="s" label="sigma_8" type="float" value="0.6159" min="0.61" max="0.9"/> <param name="z" label="z" type="float" value="1.0" min="0.0" max="1.0"/> <sanitizer sanitize="False"/> </when> </conditional> Thanks, Saba On Mar 20, 2014, at 5:35 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi all,
It may be the comparison, I've sometimes found an explicit cast to str is required in this kind of situation. So, I would try:
<command> #if str($source.source_select)=="Use_Snapshot": cM-snapshot.sh $input $output #else cM.sh $m $b $ns $w $s $z $output #end if </command>
Regards,
Peter
On Thu, Mar 20, 2014 at 10:17 AM, Nicola Soranzo <soranzo@crs4.it> wrote:
Hi Saba and Jens, ":" are not needed, they are optional, see
http://www.cheetahtemplate.org/docs/users_guide_html/users_guide.html#SECTIO...
Maybe it's a problem with the left quotes around Use_Snapshot in the #if line?
Nicola
Il 2014-03-20 06:26 Keilwagen, Jens ha scritto:
Hi Saba,
there is a syntax error in the line of the "#if". Please add ":" at the end and report whether the error still occurs.
All the best, Jens
VON: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] IM AUFTRAG VON Saba Sehrish GESENDET: Mittwoch, 19. März 2014 23:07 AN: galaxy-dev@lists.bx.psu.edu BETREFF: [galaxy-dev] Running a different command based on selection
in the tool
Hi all,
I am trying to write a tool that based on user criteria will run a different script.
In the code below, If I select Use_Snapshot, I see the right interface but somehow galaxy tries to execute the #else part and look for "m" input parameter. The example I have seen in documentation is using the script with same name in both if and else and the number of input arguments is the same as well. Any suggestions/ideas why always #else part gets executed although right interface appears based on user selection.
Thanks,
Saba
<command>
#if $source.source_select=="Use_Snapshot"
cM-snapshot.sh $input $output
#else
cM.sh $m $b $ns $w $s $z $output
#end if
</command>
<inputs>
<conditional name="source">
<param name="source_select" type="select" label="Specify the input">
<option value="Use_Snapshot">Use Snapshot</option>
<option value="Set_Values">Set Values</option>
</param>
<when value="Use_Snapshot">
<param name="input" type="data" format="dbm" size="100" label="Input Snapshot"/>
<sanitizer sanitize="False"/>
</when>
<when value="Set_Values">
<param name="m" label="Omega_m h^2" type="float" value="0.1279" min="0.120" max="0.155"/>
<param name="b" label="Omega_b h^2" type="float" value="0.0232" min="0.0215" max="0.0235"/>
<param name="ns" label="n_s" type="float" value="0.8629" min="0.85" max="1.05"/>
<param name="w" label="w" type="float" value="-1.184" min="-1.30" max="-0.70"/>
<param name="s" label="sigma_8" type="float" value="0.6159" min="0.61" max="0.9"/>
<param name="z" label="z" type="float" value="1.0" min="0.0" max="1.0"/>
<sanitizer sanitize="False"/>
</when>
</conditional>
</inputs>
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participants (5)
-
Keilwagen, Jens -
Nicola Soranzo -
Peter Cock -
Saba Sehrish -
Saba Sehrish