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galaxy-user-bounces
Hi folks,

I am trying to integrate some of my local Perl scripts into a downloaded instance of Galaxy. So far the script with a simple "in_file to out_file" format worked great, but I am having problems understanding how to treat scripts with multiple output files that share the same input argv.
for example: the script run like this in command line:

<script name> <input_name> <output_name_base>

and two files are generated from this script: "output_name_base.fasta" and "output_name_base.txt".

I am at a loss of how these parameter should be represented in the xml format, especially how the <outputs> <data name=""> tag should be filled, since in the <command> tag, there is only one $output.

Any suggestions?

thanks!
#GalaxyNoobie

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Re: Question concerning the xml file for local tools with multiple output files.

Hans-Rudolf Hotz-3
Hi Lifeng

The easiest way to execute your script will be to provide a wrapper script (written in your preferred language, eg Python, perl, etc). Call the wrapper script like this:

<command>wrapper $input $output1 $output2</command>

and define $output1 $output2 according to your needs: format="fasta", format="txt"


the wrapper will call your script and rename/move the output.


Hope this helps,
Regards, Hans-Rudolf


On Mar 25, 2014, at 3:23 AM, <[hidden email]> <[hidden email]> wrote:

>
> From: Lifeng Lin <[hidden email]>
> Date: March 25, 2014 12:58:52 AM GMT+01:00
> To: <[hidden email]>
> Subject: Question concerning the xml file for local tools with multiple output files.
>
>
> Hi folks,
>
> I am trying to integrate some of my local Perl scripts into a downloaded instance of Galaxy. So far the script with a simple "in_file to out_file" format worked great, but I am having problems understanding how to treat scripts with multiple output files that share the same input argv.
> for example: the script run like this in command line:
>
> <script name> <input_name> <output_name_base>
>
> and two files are generated from this script: "output_name_base.fasta" and "output_name_base.txt".
>
> I am at a loss of how these parameter should be represented in the xml format, especially how the <outputs> <data name=""> tag should be filled, since in the <command> tag, there is only one $output.
>
> Any suggestions?
>
> thanks!
> #GalaxyNoobie
>
>
> ___________________________________________________________
> 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/


___________________________________________________________
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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: Question concerning the xml file for local tools with multiple output files.

Lifeng Lin
works like a charm. Thank you!
I start to wonder if i should use this wrapper approach on all scripts regardless of the original input-output format for standardized integration, and possible automated integrations in the future.


On Tue, Mar 25, 2014 at 6:53 AM, Hans-Rudolf Hotz <[hidden email]> wrote:
Hi Lifeng

The easiest way to execute your script will be to provide a wrapper script (written in your preferred language, eg Python, perl, etc). Call the wrapper script like this:

<command>wrapper $input $output1 $output2</command>

and define $output1 $output2 according to your needs: format="fasta", format="txt"


the wrapper will call your script and rename/move the output.


Hope this helps,
Regards, Hans-Rudolf


On Mar 25, 2014, at 3:23 AM, <[hidden email]> <[hidden email]> wrote:

>
> From: Lifeng Lin <[hidden email]>
> Date: March 25, 2014 12:58:52 AM GMT+01:00
> To: <[hidden email]>
> Subject: Question concerning the xml file for local tools with multiple output files.
>
>
> Hi folks,
>
> I am trying to integrate some of my local Perl scripts into a downloaded instance of Galaxy. So far the script with a simple "in_file to out_file" format worked great, but I am having problems understanding how to treat scripts with multiple output files that share the same input argv.
> for example: the script run like this in command line:
>
> <script name> <input_name> <output_name_base>
>
> and two files are generated from this script: "output_name_base.fasta" and "output_name_base.txt".
>
> I am at a loss of how these parameter should be represented in the xml format, especially how the <outputs> <data name=""> tag should be filled, since in the <command> tag, there is only one $output.
>
> Any suggestions?
>
> thanks!
> #GalaxyNoobie
>
>
> ___________________________________________________________
> 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/
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Re: Question concerning the xml file for local tools with multiple output files.

Hans-Rudolf Hotz-3
Hi Lifeng

I am glad to hear it works

WRT your thoughts about using a wrapper script for each tool: I agree it might help you to standardize your tools, however it also introduces an extra step, which needs to be taken care of if  you want to change/upgrade your tool. Personally, I would only use a wrapper if it is necessary or it adds some benefits for the tool.  Others on the list might have a different opinion?

Hans-Rudolf



On Mar 25, 2014, at 3:13 PM, Lifeng Lin wrote:

> works like a charm. Thank you!
> I start to wonder if i should use this wrapper approach on all scripts regardless of the original input-output format for standardized integration, and possible automated integrations in the future.
>
>
> On Tue, Mar 25, 2014 at 6:53 AM, Hans-Rudolf Hotz <[hidden email]> wrote:
> Hi Lifeng
>
> The easiest way to execute your script will be to provide a wrapper script (written in your preferred language, eg Python, perl, etc). Call the wrapper script like this:
>
> <command>wrapper $input $output1 $output2</command>
>
> and define $output1 $output2 according to your needs: format="fasta", format="txt"
>
>
> the wrapper will call your script and rename/move the output.
>
>
> Hope this helps,
> Regards, Hans-Rudolf
>
>
> On Mar 25, 2014, at 3:23 AM, <[hidden email]> <[hidden email]> wrote:
>
> >
> > From: Lifeng Lin <[hidden email]>
> > Date: March 25, 2014 12:58:52 AM GMT+01:00
> > To: <[hidden email]>
> > Subject: Question concerning the xml file for local tools with multiple output files.
> >
> >
> > Hi folks,
> >
> > I am trying to integrate some of my local Perl scripts into a downloaded instance of Galaxy. So far the script with a simple "in_file to out_file" format worked great, but I am having problems understanding how to treat scripts with multiple output files that share the same input argv.
> > for example: the script run like this in command line:
> >
> > <script name> <input_name> <output_name_base>
> >
> > and two files are generated from this script: "output_name_base.fasta" and "output_name_base.txt".
> >
> > I am at a loss of how these parameter should be represented in the xml format, especially how the <outputs> <data name=""> tag should be filled, since in the <command> tag, there is only one $output.
> >
> > Any suggestions?
> >
> > thanks!
> > #GalaxyNoobie
> >
> >
> > ___________________________________________________________
> > 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: Question concerning the xml file for local tools with multiple output files.

Nate Coraor (nate@bx.psu.edu)
Hi Lifeng,

Another option would be the 'from_work_dir' option to the <data> tag. Have a look at the tophat repository in the Tool Shed for an example:


--nate


On Tue, Mar 25, 2014 at 11:29 AM, Hans-Rudolf Hotz <[hidden email]> wrote:
Hi Lifeng

I am glad to hear it works

WRT your thoughts about using a wrapper script for each tool: I agree it might help you to standardize your tools, however it also introduces an extra step, which needs to be taken care of if  you want to change/upgrade your tool. Personally, I would only use a wrapper if it is necessary or it adds some benefits for the tool.  Others on the list might have a different opinion?

Hans-Rudolf



On Mar 25, 2014, at 3:13 PM, Lifeng Lin wrote:

> works like a charm. Thank you!
> I start to wonder if i should use this wrapper approach on all scripts regardless of the original input-output format for standardized integration, and possible automated integrations in the future.
>
>
> On Tue, Mar 25, 2014 at 6:53 AM, Hans-Rudolf Hotz <[hidden email]> wrote:
> Hi Lifeng
>
> The easiest way to execute your script will be to provide a wrapper script (written in your preferred language, eg Python, perl, etc). Call the wrapper script like this:
>
> <command>wrapper $input $output1 $output2</command>
>
> and define $output1 $output2 according to your needs: format="fasta", format="txt"
>
>
> the wrapper will call your script and rename/move the output.
>
>
> Hope this helps,
> Regards, Hans-Rudolf
>
>
> On Mar 25, 2014, at 3:23 AM, <[hidden email]> <[hidden email]> wrote:
>
> >
> > From: Lifeng Lin <[hidden email]>
> > Date: March 25, 2014 12:58:52 AM GMT+01:00
> > To: <[hidden email]>
> > Subject: Question concerning the xml file for local tools with multiple output files.
> >
> >
> > Hi folks,
> >
> > I am trying to integrate some of my local Perl scripts into a downloaded instance of Galaxy. So far the script with a simple "in_file to out_file" format worked great, but I am having problems understanding how to treat scripts with multiple output files that share the same input argv.
> > for example: the script run like this in command line:
> >
> > <script name> <input_name> <output_name_base>
> >
> > and two files are generated from this script: "output_name_base.fasta" and "output_name_base.txt".
> >
> > I am at a loss of how these parameter should be represented in the xml format, especially how the <outputs> <data name=""> tag should be filled, since in the <command> tag, there is only one $output.
> >
> > Any suggestions?
> >
> > thanks!
> > #GalaxyNoobie
> >
> >
> > ___________________________________________________________
> > 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:
  http://galaxyproject.org/search/mailinglists/