Re: [galaxy-dev] Modifying the GATK wrappers to pick genome infomration from bam/sam dbkey attribute

2011-10-27 Thread Chorny, Ilya 
What I am trying to do is, instead of having to select the genome from a drop 
down that points to the loc file, to take the metadata.dbkey attribute of an 
input file and use it to select the genome. I want to avoid having a user of my 
workflow select a genome n times in each step of a workflow. Attached is a 
sample cufflinks_wrapper.xml and gtf_indices.loc file.

With regards to GATK, I want to edit the tools that are in the broad best 
practices workflow.

http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3

Thanks,

Ilya

From: Daniel Blankenberg [mailto:d...@bx.psu.edu]
Sent: Thursday, October 27, 2011 11:51 AM
To: Chorny, Ilya
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: Modifying the GATK wrappers to pick genome infomration from 
bam/sam dbkey attribute

Hi Ilya,

You can validate dbkeys using validators including metadata, 
dataset_metadata_in_file/data_table, unspecified_build and others.

Could you clarify what GATK tools you are trying to modify and exactly what you 
are trying accomplish? A complete example xml file, and any additional files 
(e.g. *.loc) would need to be provided to give you direction.

Thanks for using Galaxy,

Dan


On Oct 27, 2011, at 1:03 PM, Chorny, Ilya wrote:


Hi Dan,

I want to modify the wrappers to get genome information from the bam/sam 
attribute. I did this for the tophat/cufflinks wrappers. I add another option 
to select genome called attribute and then I pass $bam.metadata.dkey in the 
command line (see example below). Is this something you might be interested in? 
Can you suggest an alternative way to do this? My only concern is my inability 
to validate that the $input.metadata.dbkey exists.

Thanks,

Ilya

See example below.

#if $reference_annotation.use_ref == "Use reference annotation":
#if 
$reference_annotation.annotationSource.reference_annotation_file == "indexed":
   -G "${ filter( lambda x: str( x[0] ) == str( 
$reference_annotation.annotationSource.indices ), $__app__.tool_data_tables[ 
'gtf_index' ].get_fields() )[0][-1] }"
#else:
 #if 
$reference_annotation.annotationSource.reference_annotation_file == "attribute":
 -G "${ filter( lambda x: str( x[0] ) == str( 
$input.metadata.dbkey ), $__app__.tool_data_tables[ 'gtf_index' ].get_fields() 
)[0][-1] }"
 #else:
 -G "${reference_annotation.annotationSource.ownFile}"
 #end if
#end if
#end if



   Use a built-in index
   Use one from the 
history
   Use input bam 
metadata.dbkey attribute


  

  
  

  


  





Ilya Chorny Ph.D.
Bioinformatics Scientist I
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Work: 858.202.4582
Email: icho...@illumina.com
Website: www.illumina.com





cufflinks_wrapper.xml.diff
Description: cufflinks_wrapper.xml.diff


gtf_indices.loc
Description: gtf_indices.loc
___
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] Modifying the GATK wrappers to pick genome infomration from bam/sam dbkey attribute

2011-10-27 Thread Daniel Blankenberg 
Hi Ilya,

You can validate dbkeys using validators including metadata, 
dataset_metadata_in_file/data_table, unspecified_build and others. 

Could you clarify what GATK tools you are trying to modify and exactly what you 
are trying accomplish? A complete example xml file, and any additional files 
(e.g. *.loc) would need to be provided to give you direction.

Thanks for using Galaxy,

Dan


On Oct 27, 2011, at 1:03 PM, Chorny, Ilya wrote:

> Hi Dan,
>  
> I want to modify the wrappers to get genome information from the bam/sam 
> attribute. I did this for the tophat/cufflinks wrappers. I add another option 
> to select genome called attribute and then I pass $bam.metadata.dkey in the 
> command line (see example below). Is this something you might be interested 
> in? Can you suggest an alternative way to do this? My only concern is my 
> inability to validate that the $input.metadata.dbkey exists.
>  
> Thanks,
>  
> Ilya
>  
> See example below.
>  
> #if $reference_annotation.use_ref == "Use reference annotation":
> #if 
> $reference_annotation.annotationSource.reference_annotation_file == "indexed":
>-G "${ filter( lambda x: str( x[0] ) == str( 
> $reference_annotation.annotationSource.indices ), $__app__.tool_data_tables[ 
> 'gtf_index' ].get_fields() )[0][-1] }"
> #else:
>  #if 
> $reference_annotation.annotationSource.reference_annotation_file == 
> "attribute":
>  -G "${ filter( lambda x: str( x[0] ) == str( 
> $input.metadata.dbkey ), $__app__.tool_data_tables[ 'gtf_index' 
> ].get_fields() )[0][-1] }"
>  #else:
>  -G "${reference_annotation.annotationSource.ownFile}"
>  #end if
> #end if
> #end if
>  
> 
>  label="Please select a reference Aonnotation">
>Use a built-in 
> index
>Use one from the 
> history
>Use input bam 
> metadata.dbkey attribute
> 
> 
>   
> 
>   
>   
> 
>   
> 
> 
>   
> 
> 
>  
>  
>  
> Ilya Chorny Ph.D.
> Bioinformatics Scientist I
> Illumina, Inc.
> 9885 Towne Centre Drive
> San Diego, CA 92121
> Work: 858.202.4582
> Email: icho...@illumina.com
> Website: www.illumina.com
>  
>  

___
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] Modifying the GATK wrappers to pick genome infomration from bam/sam dbkey attribute

2011-10-27 Thread Chorny, Ilya 
Hi Dan,

I want to modify the wrappers to get genome information from the bam/sam 
attribute. I did this for the tophat/cufflinks wrappers. I add another option 
to select genome called attribute and then I pass $bam.metadata.dkey in the 
command line (see example below). Is this something you might be interested in? 
Can you suggest an alternative way to do this? My only concern is my inability 
to validate that the $input.metadata.dbkey exists.

Thanks,

Ilya

See example below.

#if $reference_annotation.use_ref == "Use reference annotation":
#if 
$reference_annotation.annotationSource.reference_annotation_file == "indexed":
   -G "${ filter( lambda x: str( x[0] ) == str( 
$reference_annotation.annotationSource.indices ), $__app__.tool_data_tables[ 
'gtf_index' ].get_fields() )[0][-1] }"
#else:
 #if 
$reference_annotation.annotationSource.reference_annotation_file == "attribute":
 -G "${ filter( lambda x: str( x[0] ) == str( 
$input.metadata.dbkey ), $__app__.tool_data_tables[ 'gtf_index' ].get_fields() 
)[0][-1] }"
 #else:
 -G "${reference_annotation.annotationSource.ownFile}"
 #end if
#end if
#end if



   Use a built-in index
   Use one from the 
history
   Use input bam 
metadata.dbkey attribute


  

  
  

  


  





Ilya Chorny Ph.D.
Bioinformatics Scientist I
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Work: 858.202.4582
Email: icho...@illumina.com
Website: www.illumina.com


___
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/