Filtering dynamic options in tool with <filter> tagset
Hi All, I’m trying to implement a tool that get a list of options through the “dynamic_options” tag. I try to filter the options that get returned with another param, but it doensn’t seem to work. my tool xml looks like this <tool id="archivetolibrary" name="Copy files" version="0.1.0"> <description>from the archive to a data library</description> <code file="list_files.py"/> <command interpreter="bash"> test.sh > $log </command> <inputs> <param name="archive_source" type="select" display="radio" label="Choose source archive"> <options from_file="archives.loc"> <column name="name" index="0"/> <column name="value" index="1"/> </options> </param> <param name="query" type="text" label="Search for files"/> <param name="selected_file" type="select" label="Choose your file" dynamic_options="list_files(archive_source)"> <filter type="param_value" ref="query" column="0" /> </param> </inputs> <outputs> <data name="log" format="txt" label="${tool.name} on ${on_string}"></data> </outputs> <tests> <test> </test> </tests> <help> </help> </tool> Anyone with experience implementing filters? (Gx 15.10 on Ubuntu 14.04.3) Thanks! Matthias
Hi Matthias I don't think you can do that...I would delegate the filtering to the 'list_files' function, i.e. by calling: list_files(archive_source,query) Regards, Hans-Rudolf On 01/27/2016 10:07 AM, Matthias De Smet wrote:
Hi All,
I’m trying to implement a tool that get a list of options through the “dynamic_options” tag. I try to filter the options that get returned with another param, but it doensn’t seem to work.
my tool xml looks like this
<tool id="archivetolibrary" name="Copy files" version="0.1.0"> <description>from the archive to a data library</description> <code file="list_files.py"/> <command interpreter="bash"> test.sh > $log </command> <inputs> <param name="archive_source" type="select" display="radio" label="Choose source archive"> <options from_file="archives.loc"> <column name="name" index="0"/> <column name="value" index="1"/> </options> </param> <param name="query" type="text" label="Search for files"/> <param name="selected_file" type="select" label="Choose your file" dynamic_options="list_files(archive_source)"> <filter type="param_value" ref="query" column="0" /> </param> </inputs> <outputs> <data name="log" format="txt" label="${tool.name} on ${on_string}"></data> </outputs> <tests> <test> </test> </tests> <help> </help> </tool>
Anyone with experience implementing filters? (Gx 15.10 on Ubuntu 14.04.3)
Thanks! Matthias ___________________________________________________________ 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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Hi Hans-Rudolf Thanks again, you’re a lifesaver! Any suggestions on how I could eliminate the <code> tag, as the wiki states it’s deprecated? I checked out <actions> but don’t see a straightforward wau to get the same results. Matthias
Op 27 jan. 2016, om 10:20 heeft Hans-Rudolf Hotz <hrh@fmi.ch> het volgende geschreven:
Hi Matthias
I don't think you can do that...I would delegate the filtering to the 'list_files' function, i.e. by calling:
list_files(archive_source,query)
Regards, Hans-Rudolf
On 01/27/2016 10:07 AM, Matthias De Smet wrote:
Hi All,
I’m trying to implement a tool that get a list of options through the “dynamic_options” tag. I try to filter the options that get returned with another param, but it doensn’t seem to work.
my tool xml looks like this
<tool id="archivetolibrary" name="Copy files" version="0.1.0"> <description>from the archive to a data library</description> <code file="list_files.py"/> <command interpreter="bash"> test.sh > $log </command> <inputs> <param name="archive_source" type="select" display="radio" label="Choose source archive"> <options from_file="archives.loc"> <column name="name" index="0"/> <column name="value" index="1"/> </options> </param> <param name="query" type="text" label="Search for files"/> <param name="selected_file" type="select" label="Choose your file" dynamic_options="list_files(archive_source)"> <filter type="param_value" ref="query" column="0" /> </param> </inputs> <outputs> <data name="log" format="txt" label="${tool.name} on ${on_string}"></data> </outputs> <tests> <test> </test> </tests> <help> </help> </tool>
Anyone with experience implementing filters? (Gx 15.10 on Ubuntu 14.04.3)
Thanks! Matthias ___________________________________________________________ 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/
On 01/27/2016 10:29 AM, Matthias De Smet wrote:
Hi Hans-Rudolf
Thanks again, you’re a lifesaver! Any suggestions on how I could eliminate the <code> tag, as the wiki states it’s deprecated?
well, it has been 'deprecated' for many years now.....
I checked out <actions> but don’t see a straightforward wau to get the same results.
same for me :( Hans-Rudolf
Matthias
Op 27 jan. 2016, om 10:20 heeft Hans-Rudolf Hotz <hrh@fmi.ch> het volgende geschreven:
Hi Matthias
I don't think you can do that...I would delegate the filtering to the 'list_files' function, i.e. by calling:
list_files(archive_source,query)
Regards, Hans-Rudolf
On 01/27/2016 10:07 AM, Matthias De Smet wrote:
Hi All,
I’m trying to implement a tool that get a list of options through the “dynamic_options” tag. I try to filter the options that get returned with another param, but it doensn’t seem to work.
my tool xml looks like this
<tool id="archivetolibrary" name="Copy files" version="0.1.0"> <description>from the archive to a data library</description> <code file="list_files.py"/> <command interpreter="bash"> test.sh > $log </command> <inputs> <param name="archive_source" type="select" display="radio" label="Choose source archive"> <options from_file="archives.loc"> <column name="name" index="0"/> <column name="value" index="1"/> </options> </param> <param name="query" type="text" label="Search for files"/> <param name="selected_file" type="select" label="Choose your file" dynamic_options="list_files(archive_source)"> <filter type="param_value" ref="query" column="0" /> </param> </inputs> <outputs> <data name="log" format="txt" label="${tool.name} on ${on_string}"></data> </outputs> <tests> <test> </test> </tests> <help> </help> </tool>
Anyone with experience implementing filters? (Gx 15.10 on Ubuntu 14.04.3)
Thanks! Matthias ___________________________________________________________ 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/
So it seems it has been deprecated a bit prematurely. Maybe the Galaxy team should “undeprecate” it untill a viable alternative is found. Anyway, thanks again! Matthias
Op 27 jan. 2016, om 10:33 heeft Hans-Rudolf Hotz <hrh@fmi.ch> het volgende geschreven:
On 01/27/2016 10:29 AM, Matthias De Smet wrote:
Hi Hans-Rudolf
Thanks again, you’re a lifesaver! Any suggestions on how I could eliminate the <code> tag, as the wiki states it’s deprecated?
well, it has been 'deprecated' for many years now.....
I checked out <actions> but don’t see a straightforward wau to get the same results.
same for me :(
Hans-Rudolf
Matthias
Op 27 jan. 2016, om 10:20 heeft Hans-Rudolf Hotz <hrh@fmi.ch> het volgende geschreven:
Hi Matthias
I don't think you can do that...I would delegate the filtering to the 'list_files' function, i.e. by calling:
list_files(archive_source,query)
Regards, Hans-Rudolf
On 01/27/2016 10:07 AM, Matthias De Smet wrote:
Hi All,
I’m trying to implement a tool that get a list of options through the “dynamic_options” tag. I try to filter the options that get returned with another param, but it doensn’t seem to work.
my tool xml looks like this
<tool id="archivetolibrary" name="Copy files" version="0.1.0"> <description>from the archive to a data library</description> <code file="list_files.py"/> <command interpreter="bash"> test.sh > $log </command> <inputs> <param name="archive_source" type="select" display="radio" label="Choose source archive"> <options from_file="archives.loc"> <column name="name" index="0"/> <column name="value" index="1"/> </options> </param> <param name="query" type="text" label="Search for files"/> <param name="selected_file" type="select" label="Choose your file" dynamic_options="list_files(archive_source)"> <filter type="param_value" ref="query" column="0" /> </param> </inputs> <outputs> <data name="log" format="txt" label="${tool.name} on ${on_string}"></data> </outputs> <tests> <test> </test> </tests> <help> </help> </tool>
Anyone with experience implementing filters? (Gx 15.10 on Ubuntu 14.04.3)
Thanks! Matthias ___________________________________________________________ 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 worries. Although it is 'deprecated' it will be not be removed until we have a good alternative. On Wed, Jan 27, 2016 at 4:36 AM, Matthias De Smet <Matthias.DeSmet@ugent.be> wrote:
So it seems it has been deprecated a bit prematurely. Maybe the Galaxy team should “undeprecate” it untill a viable alternative is found.
Anyway, thanks again!
Matthias
Op 27 jan. 2016, om 10:33 heeft Hans-Rudolf Hotz <hrh@fmi.ch> het volgende geschreven:
On 01/27/2016 10:29 AM, Matthias De Smet wrote:
Hi Hans-Rudolf
Thanks again, you’re a lifesaver! Any suggestions on how I could eliminate the <code> tag, as the wiki states it’s deprecated?
well, it has been 'deprecated' for many years now.....
I checked out <actions> but don’t see a straightforward wau to get the same results.
same for me :(
Hans-Rudolf
Matthias
Op 27 jan. 2016, om 10:20 heeft Hans-Rudolf Hotz <hrh@fmi.ch> het
volgende geschreven:
Hi Matthias
I don't think you can do that...I would delegate the filtering to the
'list_files' function, i.e. by calling:
list_files(archive_source,query)
Regards, Hans-Rudolf
On 01/27/2016 10:07 AM, Matthias De Smet wrote:
Hi All,
I’m trying to implement a tool that get a list of options through the
“dynamic_options” tag. I try to filter the options that get returned with another param, but it doensn’t seem to work.
my tool xml looks like this
<tool id="archivetolibrary" name="Copy files" version="0.1.0"> <description>from the archive to a data library</description> <code file="list_files.py"/> <command interpreter="bash"> test.sh > $log </command> <inputs> <param name="archive_source" type="select" display="radio"
label="Choose source archive">
<options from_file="archives.loc"> <column name="name" index="0"/> <column name="value" index="1"/> </options> </param> <param name="query" type="text" label="Search for files"/> <param name="selected_file" type="select" label="Choose your
file" dynamic_options="list_files(archive_source)">
<filter type="param_value" ref="query" column="0" /> </param> </inputs> <outputs> <data name="log" format="txt" label="${tool.name} on
${on_string}"></data>
</outputs> <tests> <test> </test> </tests> <help> </help> </tool>
Anyone with experience implementing filters? (Gx 15.10 on Ubuntu 14.04.3)
Thanks! Matthias ___________________________________________________________ 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/
participants (3)
-
Aysam Guerler -
Hans-Rudolf Hotz -
Matthias De Smet