Re: [galaxy-dev] multiple input files
On Tue, Oct 1, 2013 at 2:52 PM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote: Dear Peter, dear John, dear all Thanks very much. This is exactly what I need and the code changes proposed work perfectly as they are. At a short glance even the validators work as intended. Now for the optional special bonus: Is there a way to define the size of the boxes? The ones I see have 4 lines. Can I make them resizable somehow or define a larger size? (size=10 or resize=true does not seem to do the trick.) Not a very pressing issue though. +1 According to the wiki, the size attribute is only used on text input, but generalising it or adding something like lines would make sense here - and also for select parameters. It would be really nice if the user could resize the box if they wanted to - when trying to do a multiple selection from a long file list being able to seem just four entries at a time is painful. I used to have a Firefox extension to do this to arbitrary controls - very handy. 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] multiple input files
Agreed Peter, this is essential functionality. Trello card created. https://trello.com/c/J7aqer08 Thanks! -John On Fri, Oct 4, 2013 at 5:48 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Tue, Oct 1, 2013 at 2:52 PM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote: Dear Peter, dear John, dear all Thanks very much. This is exactly what I need and the code changes proposed work perfectly as they are. At a short glance even the validators work as intended. Now for the optional special bonus: Is there a way to define the size of the boxes? The ones I see have 4 lines. Can I make them resizable somehow or define a larger size? (size=10 or resize=true does not seem to do the trick.) Not a very pressing issue though. +1 According to the wiki, the size attribute is only used on text input, but generalising it or adding something like lines would make sense here - and also for select parameters. It would be really nice if the user could resize the box if they wanted to - when trying to do a multiple selection from a long file list being able to seem just four entries at a time is painful. I used to have a Firefox extension to do this to arbitrary controls - very handy. 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] multiple input files
On Tue, Oct 1, 2013 at 1:27 PM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote: Dear all We frequently find ourselves in situations where a tool needs to be run with a lot of input files. For example, run the GATK UnifiedGenotyper with easily dozens of bam files. Using the repeat in this case requires quite a bit of clicking. Is there a more conventient way fo doing this? Maybe similar to the multi-file-select that is possible for workflow inputs? I saw some older discussions on this or similar issues, but I am a bit lost what the current official stable proposed solution for this is. Thanks for your help Ulf Use param type=data multiple=true ... instead of using repeat ...param type=data .../repeat. I asked John Chilton about this recently via Twitter, and it is now on the wiki, http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax Simple example here: https://bitbucket.org/galaxyp/galaxyp-toolshed-iquant/src/tip/iquant.xml?at=default 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] multiple input files
Thanks Peter,
Yeah, looking over unified_genotyper.xml, you would probably just
want to replace:
#for $i, $input_bam in enumerate( $reference_source.input_bams ):
-d -I ${input_bam.input_bam} ${input_bam.input_bam.ext}
gatk_input_${i}
#if str( $input_bam.input_bam.metadata.bam_index ) != None:
-d ${input_bam.input_bam.metadata.bam_index}
bam_index gatk_input_${i} ##hardcode galaxy ext type as bam_index
#end if
#end for
with
#for $i, $input_bam in enumerate( $reference_source.input_bams ):
-d -I ${input_bam} ${input_bam.ext} gatk_input_${i}
#if str( $input_bam.metadata.bam_index ) != None:
-d ${input_bam.metadata.bam_index} bam_index
gatk_input_${i} ##hardcode galaxy ext type as bam_index
#end if
#end for
And:
repeat name=input_bams title=BAM file min=1
help=-I,--input_file amp;lt;input_fileamp;gt;
param name=input_bam type=data format=bam label=BAM file
validator type=unspecified_build /
validator type=dataset_metadata_in_data_table
table_name=gatk_picard_indexes metadata_name=dbkey
metadata_column=dbkey message=Sequences are not currently available
for the specified build. / !-- fixme!!! this needs to be a select
--
/param
/repeat
with
param name=input_bams type=data multiple=true
format=bam label=BAM file
validator type=unspecified_build /
validator type=dataset_metadata_in_data_table
table_name=gatk_picard_indexes metadata_name=dbkey
metadata_column=dbkey message=Sequences are not currently available
for the specified build. / !-- fixme!!! this needs to be a select
--
/param
And:
repeat name=input_bams title=BAM file min=1
help=-I,--input_file amp;lt;input_fileamp;gt;
param name=input_bam type=data format=bam label=BAM file
/param
/repeat
with
param name=input_bams multiple=true type=data
format=bam label=BAM file
/param
I have not tested these specific changes, so your millage may vary. I
have no clue if those validators in that second block are going to
work with multiple=true. If you test it out and there is some
problem, please let me know I can try to fix it.
I don't know if the Galaxy team wants to start replacing these blocks
in its tools - this change would break existing workflows built on the
unified genotyper and I am not sure the Galaxy team has any interest
in using these kind of data blocks going forward. They are working out
great for us on Galaxy-P though.
-John
On Tue, Oct 1, 2013 at 7:57 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Tue, Oct 1, 2013 at 1:27 PM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote:
Dear all
We frequently find ourselves in situations where a tool needs to be run
with a lot of input files. For example, run the GATK UnifiedGenotyper
with easily dozens of bam files.
Using the repeat in this case requires quite a bit of clicking. Is
there a more conventient way fo doing this? Maybe similar to the
multi-file-select that is possible for workflow inputs?
I saw some older discussions on this or similar issues, but I am a bit
lost what the current official stable proposed solution for this is.
Thanks for your help
Ulf
Use param type=data multiple=true ... instead of using
repeat ...param type=data .../repeat.
I asked John Chilton about this recently via Twitter, and it is
now on the wiki,
http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
Simple example here:
https://bitbucket.org/galaxyp/galaxyp-toolshed-iquant/src/tip/iquant.xml?at=default
Peter
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___
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Re: [galaxy-dev] multiple input files
Hi Ulf, What I do: 1. make a history, doing the steps you want to do on one input file 2. create a workflow of that history 3. assemble all input files in one history 4. run the workflow and select the multiple input files to run the workflow on. 5. Optionally: send the results to a new history, for every input file you will get a new history, properly named. Hope this helps, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 10/01/2013 02:27 PM, Ulf Schaefer wrote: Dear all We frequently find ourselves in situations where a tool needs to be run with a lot of input files. For example, run the GATK UnifiedGenotyper with easily dozens of bam files. Using the repeat in this case requires quite a bit of clicking. Is there a more conventient way fo doing this? Maybe similar to the multi-file-select that is possible for workflow inputs? I saw some older discussions on this or similar issues, but I am a bit lost what the current official stable proposed solution for this is. Thanks for your help Ulf ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE ** ___ 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/
Re: [galaxy-dev] multiple input files
Sorry, my answer doesn't fit your question. :-) J Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 10/01/2013 03:08 PM, Joachim Jacob | VIB | wrote: Hi Ulf, What I do: 1. make a history, doing the steps you want to do on one input file 2. create a workflow of that history 3. assemble all input files in one history 4. run the workflow and select the multiple input files to run the workflow on. 5. Optionally: send the results to a new history, for every input file you will get a new history, properly named. Hope this helps, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 10/01/2013 02:27 PM, Ulf Schaefer wrote: Dear all We frequently find ourselves in situations where a tool needs to be run with a lot of input files. For example, run the GATK UnifiedGenotyper with easily dozens of bam files. Using the repeat in this case requires quite a bit of clicking. Is there a more conventient way fo doing this? Maybe similar to the multi-file-select that is possible for workflow inputs? I saw some older discussions on this or similar issues, but I am a bit lost what the current official stable proposed solution for this is. Thanks for your help Ulf ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE ** ___ 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/
Re: [galaxy-dev] multiple input files
Dear Peter, dear John, dear all
Thanks very much. This is exactly what I need and the code changes
proposed work perfectly as they are. At a short glance even the
validators work as intended.
Now for the optional special bonus:
Is there a way to define the size of the boxes? The ones I see have 4
lines. Can I make them resizable somehow or define a larger size?
(size=10 or resize=true does not seem to do the trick.) Not a very
pressing issue though.
@Joachim: I am using the same approach elsewhere, but the difference is
that it runs a tool multiple times, instead of running it once on
multiple inputs. But thanks anyway.
Cheers
Ulf
On 01/10/13 14:08, John Chilton wrote:
Thanks Peter,
Yeah, looking over unified_genotyper.xml, you would probably just
want to replace:
#for $i, $input_bam in enumerate( $reference_source.input_bams ):
-d -I ${input_bam.input_bam} ${input_bam.input_bam.ext}
gatk_input_${i}
#if str( $input_bam.input_bam.metadata.bam_index ) != None:
-d ${input_bam.input_bam.metadata.bam_index}
bam_index gatk_input_${i} ##hardcode galaxy ext type as bam_index
#end if
#end for
with
#for $i, $input_bam in enumerate( $reference_source.input_bams ):
-d -I ${input_bam} ${input_bam.ext} gatk_input_${i}
#if str( $input_bam.metadata.bam_index ) != None:
-d ${input_bam.metadata.bam_index} bam_index
gatk_input_${i} ##hardcode galaxy ext type as bam_index
#end if
#end for
And:
repeat name=input_bams title=BAM file min=1
help=-I,--input_file amp;lt;input_fileamp;gt;
param name=input_bam type=data format=bam label=BAM
file
validator type=unspecified_build /
validator type=dataset_metadata_in_data_table
table_name=gatk_picard_indexes metadata_name=dbkey
metadata_column=dbkey message=Sequences are not currently available
for the specified build. / !-- fixme!!! this needs to be a select
--
/param
/repeat
with
param name=input_bams type=data multiple=true
format=bam label=BAM file
validator type=unspecified_build /
validator type=dataset_metadata_in_data_table
table_name=gatk_picard_indexes metadata_name=dbkey
metadata_column=dbkey message=Sequences are not currently available
for the specified build. / !-- fixme!!! this needs to be a select
--
/param
And:
repeat name=input_bams title=BAM file min=1
help=-I,--input_file amp;lt;input_fileamp;gt;
param name=input_bam type=data format=bam label=BAM
file
/param
/repeat
with
param name=input_bams multiple=true type=data
format=bam label=BAM file
/param
I have not tested these specific changes, so your millage may vary. I
have no clue if those validators in that second block are going to
work with multiple=true. If you test it out and there is some
problem, please let me know I can try to fix it.
I don't know if the Galaxy team wants to start replacing these blocks
in its tools - this change would break existing workflows built on the
unified genotyper and I am not sure the Galaxy team has any interest
in using these kind of data blocks going forward. They are working out
great for us on Galaxy-P though.
-John
On Tue, Oct 1, 2013 at 7:57 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Tue, Oct 1, 2013 at 1:27 PM, Ulf Schaefer ulf.schae...@phe.gov.uk wrote:
Dear all
We frequently find ourselves in situations where a tool needs to be run
with a lot of input files. For example, run the GATK UnifiedGenotyper
with easily dozens of bam files.
Using the repeat in this case requires quite a bit of clicking. Is
there a more conventient way fo doing this? Maybe similar to the
multi-file-select that is possible for workflow inputs?
I saw some older discussions on this or similar issues, but I am a bit
lost what the current official stable proposed solution for this is.
Thanks for your help
Ulf
Use param type=data multiple=true ... instead of using
repeat ...param type=data .../repeat.
I asked John Chilton about this recently via Twitter, and it is
now on the wiki,
http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
Simple example here:
https://bitbucket.org/galaxyp/galaxyp-toolshed-iquant/src/tip/iquant.xml?at=default
Peter
___
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and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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**
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