Managing large database lists in tool wrappers?

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Managing large database lists in tool wrappers?

Smithies, Russell

Does anyone have a workable solution to managing and displaying large lists in tool wrappers?

eg.  a database list containing hundreds of enteries in the blast+ tool? (we have 1,056 different blast databases).

As a work-around we’ve split our blast databases into species (eg cow, sheep, fungus, clover, fish, rice, etc)  then faked a multi-select to pull in those sub-database files with conditional selectors like this:

 

  <conditional name="db_opts">

        <param name="db_opts_selector" type="select" label="Nucleotide Database Type">

          <option value="pub" selected="True">Pub Databases</option>

          <option value="cattle">Cattle Databases</option>

          <option value="sheep">Sheep Databases</option>

          <option value="deer">Deer Databases</option>

          <option value="ruminant">Ruminant Databases</option>

          <option value="dog">Dog Databases</option>

          <option value="fungi">Fungi Databases</option>

          <option value="invertebrates">Invertebrates Databases</option>

          <option value="microarrays">Microarrays Databases</option>

          <option value="marsupials">Marsupials Databases</option>

          <option value="rodent">Rodent Databases</option>

          <option value="viruses">Viruses Databases</option>

          <option value="human">Human Databases</option>

          <option value="microarrays">Microarrays Databases</option>

            </param>

 

            <when value="ruminant">

                <param name="database" type="select" label="Ruminant Nucleotide BLAST database" help="">

                    <options from_file="blastdb.ruminant.loc">

                      <column name="value" index="0"/>

                      <column name="name" index="1"/>

                      <column name="path" index="2"/>

                    </options>

                </param>

                <param name="subject" type="hidden" value="" />

            </when>

 

 

            <when value="misc">

                <param name="database" type="select" label="Misc Nucleotide BLAST database" help="">

                    <options from_file="blastdb.misc.loc">

                      <column name="value" index="0"/>

                      <column name="name" index="1"/>

                      <column name="path" index="2"/>

                    </options>

                </param>

                <param name="subject" type="hidden" value="" />

            </when>

 

 

We end up with a lot of duplication between tool wrappers (I’ve never managed to get an <include> tag working)  and these aren’t exactly simple to maintain so does anyone have a better solution?

I had thought about tacking an extra field onto the .loc files with a “species” and doing some grouping with that but haven’t progressed that idea very far yet.

 

Any suggestions greatly appreciated J

 

Thanx,

 

--Russell


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Re: Managing large database lists in tool wrappers?

Björn Grüning-3
Hi Russell,

would something like a http://ivaynberg.github.io/select2/ field work
for you?
What do you mean with <include> tags? Are you aware of Galaxy macros?
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#Direct_XML_Macros

Cheers,
Bjoern

Am 31.03.2014 22:58, schrieb Smithies, Russell:

> Does anyone have a workable solution to managing and displaying large lists in tool wrappers?
> eg.  a database list containing hundreds of enteries in the blast+ tool? (we have 1,056 different blast databases).
> As a work-around we've split our blast databases into species (eg cow, sheep, fungus, clover, fish, rice, etc)  then faked a multi-select to pull in those sub-database files with conditional selectors like this:
>
>    <conditional name="db_opts">
>          <param name="db_opts_selector" type="select" label="Nucleotide Database Type">
>            <option value="pub" selected="True">Pub Databases</option>
>            <option value="cattle">Cattle Databases</option>
>            <option value="sheep">Sheep Databases</option>
>            <option value="deer">Deer Databases</option>
>            <option value="ruminant">Ruminant Databases</option>
>            <option value="dog">Dog Databases</option>
>            <option value="fungi">Fungi Databases</option>
>            <option value="invertebrates">Invertebrates Databases</option>
>            <option value="microarrays">Microarrays Databases</option>
>            <option value="marsupials">Marsupials Databases</option>
>            <option value="rodent">Rodent Databases</option>
>            <option value="viruses">Viruses Databases</option>
>            <option value="human">Human Databases</option>
>            <option value="microarrays">Microarrays Databases</option>
>              </param>
>
>              <when value="ruminant">
>                  <param name="database" type="select" label="Ruminant Nucleotide BLAST database" help="">
>                      <options from_file="blastdb.ruminant.loc">
>                        <column name="value" index="0"/>
>                        <column name="name" index="1"/>
>                        <column name="path" index="2"/>
>                      </options>
>                  </param>
>                  <param name="subject" type="hidden" value="" />
>              </when>
>
>
>              <when value="misc">
>                  <param name="database" type="select" label="Misc Nucleotide BLAST database" help="">
>                      <options from_file="blastdb.misc.loc">
>                        <column name="value" index="0"/>
>                        <column name="name" index="1"/>
>                        <column name="path" index="2"/>
>                      </options>
>                  </param>
>                  <param name="subject" type="hidden" value="" />
>              </when>
>
>
> We end up with a lot of duplication between tool wrappers (I've never managed to get an <include> tag working)  and these aren't exactly simple to maintain so does anyone have a better solution?
> I had thought about tacking an extra field onto the .loc files with a "species" and doing some grouping with that but haven't progressed that idea very far yet.
>
> Any suggestions greatly appreciated :)
>
> Thanx,
>
> --Russell
>
>
>
> ___________________________________________________________
> 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:
>    http://lists.bx.psu.edu/
>
> 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:
  http://lists.bx.psu.edu/

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Re: Managing large database lists in tool wrappers?

Smithies, Russell
Hi Bjoern,
Yes I'm aware of the macros but I've never managed to get them to work ;-(

What I'd like is something like a php include tag to pull the contents of a whole file into another file so I'm not repeating myself eg. for the database lists in the megablast, blastn, and tblastn wrappers.  

Those select fields are nice, and in "ordinary" html and JQuery you can do grouping but as far as I can tell it's not possible with Galaxy/Cheetah XML templating - though we are a few versions behind so may have overlooked recent updates.

Thanx for your suggestions,

--Russell

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Björn Grüning
Sent: Tuesday, 1 April 2014 10:19 a.m.
To: [hidden email]
Subject: Re: [galaxy-dev] Managing large database lists in tool wrappers?

Hi Russell,

would something like a http://ivaynberg.github.io/select2/ field work for you?
What do you mean with <include> tags? Are you aware of Galaxy macros?
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#Direct_XML_Macros

Cheers,
Bjoern

Am 31.03.2014 22:58, schrieb Smithies, Russell:

> Does anyone have a workable solution to managing and displaying large lists in tool wrappers?
> eg.  a database list containing hundreds of enteries in the blast+ tool? (we have 1,056 different blast databases).
> As a work-around we've split our blast databases into species (eg cow, sheep, fungus, clover, fish, rice, etc)  then faked a multi-select to pull in those sub-database files with conditional selectors like this:
>
>    <conditional name="db_opts">
>          <param name="db_opts_selector" type="select" label="Nucleotide Database Type">
>            <option value="pub" selected="True">Pub Databases</option>
>            <option value="cattle">Cattle Databases</option>
>            <option value="sheep">Sheep Databases</option>
>            <option value="deer">Deer Databases</option>
>            <option value="ruminant">Ruminant Databases</option>
>            <option value="dog">Dog Databases</option>
>            <option value="fungi">Fungi Databases</option>
>            <option value="invertebrates">Invertebrates Databases</option>
>            <option value="microarrays">Microarrays Databases</option>
>            <option value="marsupials">Marsupials Databases</option>
>            <option value="rodent">Rodent Databases</option>
>            <option value="viruses">Viruses Databases</option>
>            <option value="human">Human Databases</option>
>            <option value="microarrays">Microarrays Databases</option>
>              </param>
>
>              <when value="ruminant">
>                  <param name="database" type="select" label="Ruminant Nucleotide BLAST database" help="">
>                      <options from_file="blastdb.ruminant.loc">
>                        <column name="value" index="0"/>
>                        <column name="name" index="1"/>
>                        <column name="path" index="2"/>
>                      </options>
>                  </param>
>                  <param name="subject" type="hidden" value="" />
>              </when>
>
>
>              <when value="misc">
>                  <param name="database" type="select" label="Misc Nucleotide BLAST database" help="">
>                      <options from_file="blastdb.misc.loc">
>                        <column name="value" index="0"/>
>                        <column name="name" index="1"/>
>                        <column name="path" index="2"/>
>                      </options>
>                  </param>
>                  <param name="subject" type="hidden" value="" />
>              </when>
>
>
> We end up with a lot of duplication between tool wrappers (I've never managed to get an <include> tag working)  and these aren't exactly simple to maintain so does anyone have a better solution?
> I had thought about tacking an extra field onto the .loc files with a "species" and doing some grouping with that but haven't progressed that idea very far yet.
>
> Any suggestions greatly appreciated :)
>
> Thanx,
>
> --Russell
>
>
>
> ___________________________________________________________
> 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:
>    http://lists.bx.psu.edu/
>
> 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:
  http://lists.bx.psu.edu/

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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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Re: Managing large database lists in tool wrappers?

Björn Grüning-3
Hi Russell,

Am 31.03.2014 23:46, schrieb Smithies, Russell:
> Hi Bjoern,
> Yes I'm aware of the macros but I've never managed to get them to work ;-(

Lets try to get them to work. It will do exactly what you want.
The Homer Tools should be a easy enough to get you started:

https://github.com/bgruening/galaxytools/tree/master/homer/tools


> What I'd like is something like a php include tag to pull the contents of a whole file into another file so I'm not repeating myself eg. for the database lists in the megablast, blastn, and tblastn wrappers.
>
> Those select fields are nice, and in "ordinary" html and JQuery you can do grouping but as far as I can tell it's not possible with Galaxy/Cheetah XML templating -
> though we are a few versions behind so may have overlooked recent updates.

Not yet, but I think it would be easy to implement it. It's used in
other areas of Galaxy a lot.

Ciao,
Bjoern

> Thanx for your suggestions,
>
> --Russell
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On Behalf Of Björn Grüning
> Sent: Tuesday, 1 April 2014 10:19 a.m.
> To: [hidden email]
> Subject: Re: [galaxy-dev] Managing large database lists in tool wrappers?
>
> Hi Russell,
>
> would something like a http://ivaynberg.github.io/select2/ field work for you?
> What do you mean with <include> tags? Are you aware of Galaxy macros?
> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#Direct_XML_Macros
>
> Cheers,
> Bjoern
>
> Am 31.03.2014 22:58, schrieb Smithies, Russell:
>> Does anyone have a workable solution to managing and displaying large lists in tool wrappers?
>> eg.  a database list containing hundreds of enteries in the blast+ tool? (we have 1,056 different blast databases).
>> As a work-around we've split our blast databases into species (eg cow, sheep, fungus, clover, fish, rice, etc)  then faked a multi-select to pull in those sub-database files with conditional selectors like this:
>>
>>     <conditional name="db_opts">
>>           <param name="db_opts_selector" type="select" label="Nucleotide Database Type">
>>             <option value="pub" selected="True">Pub Databases</option>
>>             <option value="cattle">Cattle Databases</option>
>>             <option value="sheep">Sheep Databases</option>
>>             <option value="deer">Deer Databases</option>
>>             <option value="ruminant">Ruminant Databases</option>
>>             <option value="dog">Dog Databases</option>
>>             <option value="fungi">Fungi Databases</option>
>>             <option value="invertebrates">Invertebrates Databases</option>
>>             <option value="microarrays">Microarrays Databases</option>
>>             <option value="marsupials">Marsupials Databases</option>
>>             <option value="rodent">Rodent Databases</option>
>>             <option value="viruses">Viruses Databases</option>
>>             <option value="human">Human Databases</option>
>>             <option value="microarrays">Microarrays Databases</option>
>>               </param>
>>
>>               <when value="ruminant">
>>                   <param name="database" type="select" label="Ruminant Nucleotide BLAST database" help="">
>>                       <options from_file="blastdb.ruminant.loc">
>>                         <column name="value" index="0"/>
>>                         <column name="name" index="1"/>
>>                         <column name="path" index="2"/>
>>                       </options>
>>                   </param>
>>                   <param name="subject" type="hidden" value="" />
>>               </when>
>>
>>
>>               <when value="misc">
>>                   <param name="database" type="select" label="Misc Nucleotide BLAST database" help="">
>>                       <options from_file="blastdb.misc.loc">
>>                         <column name="value" index="0"/>
>>                         <column name="name" index="1"/>
>>                         <column name="path" index="2"/>
>>                       </options>
>>                   </param>
>>                   <param name="subject" type="hidden" value="" />
>>               </when>
>>
>>
>> We end up with a lot of duplication between tool wrappers (I've never managed to get an <include> tag working)  and these aren't exactly simple to maintain so does anyone have a better solution?
>> I had thought about tacking an extra field onto the .loc files with a "species" and doing some grouping with that but haven't progressed that idea very far yet.
>>
>> Any suggestions greatly appreciated :)
>>
>> Thanx,
>>
>> --Russell
>>
>>
>>
>> ___________________________________________________________
>> 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:
>>     http://lists.bx.psu.edu/
>>
>> 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:
>    http://lists.bx.psu.edu/
>
> 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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Re: Managing large database lists in tool wrappers?

Smithies, Russell
Those macros look great and are exactly what I want :-)

Thanx,

--Russell

-----Original Message-----
From: Björn Grüning [mailto:[hidden email]]
Sent: Tuesday, 1 April 2014 11:07 a.m.
To: Smithies, Russell; Björn Grüning; [hidden email]
Subject: Re: [galaxy-dev] Managing large database lists in tool wrappers?

Hi Russell,

Am 31.03.2014 23:46, schrieb Smithies, Russell:
> Hi Bjoern,
> Yes I'm aware of the macros but I've never managed to get them to work
> ;-(

Lets try to get them to work. It will do exactly what you want.
The Homer Tools should be a easy enough to get you started:

https://github.com/bgruening/galaxytools/tree/master/homer/tools


> What I'd like is something like a php include tag to pull the contents of a whole file into another file so I'm not repeating myself eg. for the database lists in the megablast, blastn, and tblastn wrappers.
>
> Those select fields are nice, and in "ordinary" html and JQuery you
> can do grouping but as far as I can tell it's not possible with Galaxy/Cheetah XML templating - though we are a few versions behind so may have overlooked recent updates.

Not yet, but I think it would be easy to implement it. It's used in other areas of Galaxy a lot.

Ciao,
Bjoern

> Thanx for your suggestions,
>
> --Russell
>
> -----Original Message-----
> From: [hidden email]
> [mailto:[hidden email]] On Behalf Of Björn
> Grüning
> Sent: Tuesday, 1 April 2014 10:19 a.m.
> To: [hidden email]
> Subject: Re: [galaxy-dev] Managing large database lists in tool wrappers?
>
> Hi Russell,
>
> would something like a http://ivaynberg.github.io/select2/ field work for you?
> What do you mean with <include> tags? Are you aware of Galaxy macros?
> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#Direct_XML
> _Macros
>
> Cheers,
> Bjoern
>
> Am 31.03.2014 22:58, schrieb Smithies, Russell:
>> Does anyone have a workable solution to managing and displaying large lists in tool wrappers?
>> eg.  a database list containing hundreds of enteries in the blast+ tool? (we have 1,056 different blast databases).
>> As a work-around we've split our blast databases into species (eg cow, sheep, fungus, clover, fish, rice, etc)  then faked a multi-select to pull in those sub-database files with conditional selectors like this:
>>
>>     <conditional name="db_opts">
>>           <param name="db_opts_selector" type="select" label="Nucleotide Database Type">
>>             <option value="pub" selected="True">Pub Databases</option>
>>             <option value="cattle">Cattle Databases</option>
>>             <option value="sheep">Sheep Databases</option>
>>             <option value="deer">Deer Databases</option>
>>             <option value="ruminant">Ruminant Databases</option>
>>             <option value="dog">Dog Databases</option>
>>             <option value="fungi">Fungi Databases</option>
>>             <option value="invertebrates">Invertebrates Databases</option>
>>             <option value="microarrays">Microarrays Databases</option>
>>             <option value="marsupials">Marsupials Databases</option>
>>             <option value="rodent">Rodent Databases</option>
>>             <option value="viruses">Viruses Databases</option>
>>             <option value="human">Human Databases</option>
>>             <option value="microarrays">Microarrays Databases</option>
>>               </param>
>>
>>               <when value="ruminant">
>>                   <param name="database" type="select" label="Ruminant Nucleotide BLAST database" help="">
>>                       <options from_file="blastdb.ruminant.loc">
>>                         <column name="value" index="0"/>
>>                         <column name="name" index="1"/>
>>                         <column name="path" index="2"/>
>>                       </options>
>>                   </param>
>>                   <param name="subject" type="hidden" value="" />
>>               </when>
>>
>>
>>               <when value="misc">
>>                   <param name="database" type="select" label="Misc Nucleotide BLAST database" help="">
>>                       <options from_file="blastdb.misc.loc">
>>                         <column name="value" index="0"/>
>>                         <column name="name" index="1"/>
>>                         <column name="path" index="2"/>
>>                       </options>
>>                   </param>
>>                   <param name="subject" type="hidden" value="" />
>>               </when>
>>
>>
>> We end up with a lot of duplication between tool wrappers (I've never managed to get an <include> tag working)  and these aren't exactly simple to maintain so does anyone have a better solution?
>> I had thought about tacking an extra field onto the .loc files with a "species" and doing some grouping with that but haven't progressed that idea very far yet.
>>
>> Any suggestions greatly appreciated :)
>>
>> Thanx,
>>
>> --Russell
>>
>>
>>
>> ___________________________________________________________
>> 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:
>>     http://lists.bx.psu.edu/
>>
>> 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:
>    http://lists.bx.psu.edu/
>
> 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:
  http://lists.bx.psu.edu/

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Re: Managing large database lists in tool wrappers?

Peter Cock
In reply to this post by Björn Grüning-3
> On 31.03.2014 22:58,  Smithies, Russell:
>>
>> Does anyone have a workable solution to managing and
>> displaying large lists in tool wrappers?
>> eg.  a database list containing hundreds of enteries in the
>> blast+ tool? (we have 1,056 different blast databases).
>>

On Mon, Mar 31, 2014 at 10:18 PM, Björn Grüning
<[hidden email]> wrote:
>
> Hi Russell,
>
> would something like a http://ivaynberg.github.io/select2/ field
> work for you?

Which bit of that do you mean Bjoern? Galaxy already does searching
within the drop down box (when the list is above some threshold
in length) which is very handy.

Mind you, we currently have under a hundred BLAST databases
defined in our *.loc files, so this is an order of magnitude less
than Russell's setup.

> What do you mean with <include> tags? Are you aware of Galaxy macros?
> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#Direct_XML_Macros
>
> Cheers,
> Bjoern

Since it looks like you are modifying the BLAST+ wrappers, they
are already using Galaxy macros - you probably only need to
change the ncbi_macros.xml file once and have this work on
all of BLASTP, BLASTN, etc.

i.e. Modify the input_conditional_nucleotide_db and
input_conditional_protein_db definitions (and potentially the
token @BLAST_DB_SUBJECT@ where those parameters
are inserted in the the Cheetah command line template):

https://github.com/peterjc/galaxy_blast/blob/master/tools/ncbi_blast_plus/ncbi_macros.xml

Regards,

Peter

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Re: Managing large database lists in tool wrappers?

Björn Grüning-3
Hi,

>> On 31.03.2014 22:58,  Smithies, Russell:
>>>
>>> Does anyone have a workable solution to managing and
>>> displaying large lists in tool wrappers?
>>> eg.  a database list containing hundreds of enteries in the
>>> blast+ tool? (we have 1,056 different blast databases).
>>>
>
> On Mon, Mar 31, 2014 at 10:18 PM, Björn Grüning
> <[hidden email]> wrote:
>>
>> Hi Russell,
>>
>> would something like a http://ivaynberg.github.io/select2/ field
>> work for you?
>
> Which bit of that do you mean Bjoern? Galaxy already does searching
> within the drop down box (when the list is above some threshold
> in length) which is very handy.

Yes, that was my intention. To point out that something like that should
be possible. It new for me that there is a threshold to enable that
mechanism.

> Mind you, we currently have under a hundred BLAST databases
> defined in our *.loc files, so this is an order of magnitude less
> than Russell's setup.

We also have only 3x. So no problem until now.

Ciao,
Bjoern

>> What do you mean with <include> tags? Are you aware of Galaxy macros?
>> https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#Direct_XML_Macros
>>
>> Cheers,
>> Bjoern
>
> Since it looks like you are modifying the BLAST+ wrappers, they
> are already using Galaxy macros - you probably only need to
> change the ncbi_macros.xml file once and have this work on
> all of BLASTP, BLASTN, etc.
>
> i.e. Modify the input_conditional_nucleotide_db and
> input_conditional_protein_db definitions (and potentially the
> token @BLAST_DB_SUBJECT@ where those parameters
> are inserted in the the Cheetah command line template):
>
> https://github.com/peterjc/galaxy_blast/blob/master/tools/ncbi_blast_plus/ncbi_macros.xml
>
> Regards,
>
> Peter
>
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