Re: [galaxy-dev] Components

[Peter Cock]

On Tue, Jun 7, 2011 at 9:24 AM, Mariette jmari...@toulouse.inra.fr wrote:

 Thanks for the answer,

 so I tryed to write a wrapper, but the main script is not recognize.
 When I'm calling my wrapper in the xml file, I don't have to specify
 the full path but then from my wrapper if I want to call my main script
 I can't if this one is not on the PATH ? the wrapper current directory
 is the job_working_directory, there is anyway to access my main script
 just like it's done for the wrapper ?

Generally put the wrapper script next to your tool XML file, and don't
prefix it with any path in the command tag in the XML, e.g.

/opt/galaxy/tools/mariette/my_tool.xml
/opt/galaxy/tools/mariette/my_tool.sh

(or my_tool.py or my_tool.pl etc depending on what language you used)

Your wrapper script then has to call the real executable, and the
normal way to do this on Unix is to have it on the PATH. You could
also hard code an absolute path.

Peter
___
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/

Re: [galaxy-dev] Components

[Peter Cock]

On Tue, Jun 7, 2011 at 10:56 AM, Mariette jmari...@toulouse.inra.fr wrote:

 Thanks for the answer,
 Still considering the number of outputed files problem. In my script I know
 that if
 a cleaning option is set 2 other files will be created, so I check if the
 option is asked by the
 user and try this :

  outputs
   data name=log format=txt /
   #if $clean_pairends.clean_pairends_select==y:
       data name=output format=input/
   #end if
  /outputs

 but this is not working ... there is a way to do what I want ?
 thx
 Jerome

The #if stuff is Cheetah syntax, and only applies within the command
tag - not to the XML file in general.

You probably want a conditional output using when, see:
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax

Peter

___
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/

Re: [galaxy-dev] Components

[Mariette]

Thanks for the answer,

so I tryed to write a wrapper, but the main script is not recognize.
When I'm calling my wrapper in the xml file, I don't have to specify
the full path but then from my wrapper if I want to call my main script
I can't if this one is not on the PATH ? the wrapper current directory
is the job_working_directory, there is anyway to access my main script
just like it's done for the wrapper ?

thanks for your answer,
Jerome





Peter Cock a écrit :

On Mon, Jun 6, 2011 at 2:45 PM, Mariette jmari...@toulouse.inra.fr wrote:
  

Hi everyone,

I'm new in galaxy and I want to create a component, so I have multiple
questions.
The component executes a script which takes different formats :
fasta|fastq|sff. As output it takes a folder, to do so I used the
extra_files_path attribute of an output data
(--out='$output.extra_files_path'). The result file is stored in this folder
with the log file and should be in the same format as the input one.
I wrote the xml file and it works just fine, however as it's a folder there
is no way to use the result file(s) for further analysis. How can I manage
this ?



I use a wrapper script which moves the output file from the sub-directory
to the location Galaxy requested.

Regarding the file format, if you only have one input file you can use
format=input, otherwise use the change_format tag in the XML.

  

Also it can happen that there is more than 1 file outputted, how can I
manage multiple outputs ?

An other question about the input format, I have an option to the script to
specify the format. I saw there is auto-format detection routines in galaxy,
there is a way so I can call them to automatically complete this option ?



Normally the wrapper specifies the output format explicitly.

Peter
___
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/
  


___
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/

Re: [galaxy-dev] Components

[Mariette]

Thanks for the answer,
Still considering the number of outputed files problem. In my script I 
know that if
a cleaning option is set 2 other files will be created, so I check if 
the option is asked by the

user and try this :

 outputs
   data name=log format=txt /
   #if $clean_pairends.clean_pairends_select==y:
   data name=output format=input/
   #end if
 /outputs

but this is not working ... there is a way to do what I want ?
thx
Jerome




Peter Cock a écrit :

On Tue, Jun 7, 2011 at 9:24 AM, Mariette jmari...@toulouse.inra.fr wrote:
  

Thanks for the answer,

so I tryed to write a wrapper, but the main script is not recognize.
When I'm calling my wrapper in the xml file, I don't have to specify
the full path but then from my wrapper if I want to call my main script
I can't if this one is not on the PATH ? the wrapper current directory
is the job_working_directory, there is anyway to access my main script
just like it's done for the wrapper ?



Generally put the wrapper script next to your tool XML file, and don't
prefix it with any path in the command tag in the XML, e.g.

/opt/galaxy/tools/mariette/my_tool.xml
/opt/galaxy/tools/mariette/my_tool.sh

(or my_tool.py or my_tool.pl etc depending on what language you used)

Your wrapper script then has to call the real executable, and the
normal way to do this on Unix is to have it on the PATH. You could
also hard code an absolute path.

Peter
___
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/
  


___
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/

Re: [galaxy-dev] Components

[Mariette]

So I tryed an other way to access the value :

  data name=out_pe_fasta format=fasta
  filter${clean_pairends.clean_pairends_select} == y/filter
  /data

but it's not working either ... I tryed to add a label to the data like 
this :


  data name=out_pe_fasta format=fasta 
label=${clean_pairends.clean_pairends_select}

  filter${clean_pairends.clean_pairends_select} == y/filter
  /data

the data file is created with a label n ! Is it not weird ?

Jerome




Mariette a écrit :


Thanks this is what I was looking for !!
I succeded to make it work when checking the value on a simple param 
using the name like this


inputs
param name=qual_file type=data format=qual optional=true 
label=Quality reads file (if input is a fasta) /

/input
...
outputs
data name=out_qual format=qual
 filterqual_file != None/filter
/data
/outputs

however when I'm in a conditional tag like this, I tryed :

inputs
conditional name=clean_pairends
param name=clean_pairends_select type=select label=Clean 
pairends

  option value=yYes/option
  option selected=true value=nNo/option
/param
when value=y
  param name=border_limit type=integer size=10 
value=70 label=Minimal length between the spacer and the read 
extremity/
  param name=missmatch type=integer size=10 value=10 
label=Limit of missmatch/

 /when
 when value=n
 /when
/conditional
/input
...
outputs
data name=out_pe_fasta format=fasta
  filterclean_pairends.clean_pairends_select == y/filter
/data


but it's not working ... it looks like between filter tag I should 
provide a python test, am I missing something ?

thx,
Jerome



Peter Cock a écrit :
On Tue, Jun 7, 2011 at 11:38 AM, Mariette jmari...@toulouse.inra.fr 
wrote:
 

I can only see the usage of the when tag into the outputs
to change format, is that correct ?




On re-reading the wiki page, yes, I think you are right. I should have
said filter with data, as in tools/filters/sff_extractor.xml

Peter
___
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/
  


___
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/


___
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/

[galaxy-dev] Components

[Mariette]

Hi everyone,

I'm new in galaxy and I want to create a component, so I have multiple 
questions.
The component executes a script which takes different formats : 
fasta|fastq|sff. As output it takes a folder, to do so I used the 
extra_files_path attribute of an output data 
(--out='$output.extra_files_path'). The result file is stored in this 
folder with the log file and should be in the same format as the input one.
I wrote the xml file and it works just fine, however as it's a folder 
there is no way to use the result file(s) for further analysis. How can 
I manage this ?
Also it can happen that there is more than 1 file outputted, how can I 
manage multiple outputs ?


An other question about the input format, I have an option to the script 
to specify the format. I saw there is auto-format detection routines in 
galaxy, there is a way so I can call them to automatically complete this 
option ?


thx,
Jerome
___
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/

Re: [galaxy-dev] Components

[Peter Cock]

On Mon, Jun 6, 2011 at 2:45 PM, Mariette jmari...@toulouse.inra.fr wrote:
 Hi everyone,

 I'm new in galaxy and I want to create a component, so I have multiple
 questions.
 The component executes a script which takes different formats :
 fasta|fastq|sff. As output it takes a folder, to do so I used the
 extra_files_path attribute of an output data
 (--out='$output.extra_files_path'). The result file is stored in this folder
 with the log file and should be in the same format as the input one.
 I wrote the xml file and it works just fine, however as it's a folder there
 is no way to use the result file(s) for further analysis. How can I manage
 this ?

I use a wrapper script which moves the output file from the sub-directory
to the location Galaxy requested.

Regarding the file format, if you only have one input file you can use
format=input, otherwise use the change_format tag in the XML.

 Also it can happen that there is more than 1 file outputted, how can I
 manage multiple outputs ?

 An other question about the input format, I have an option to the script to
 specify the format. I saw there is auto-format detection routines in galaxy,
 there is a way so I can call them to automatically complete this option ?

Normally the wrapper specifies the output format explicitly.

Peter
___
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/