Re: [galaxy-dev] Multiple output tools in Workflow

[Calogero Zarbo]

Hello Peter,

Thanks for your answer.

I tried your come but I am still not able to make it work the way I want.
I mean that in the workflow design page, when I switch the parameter, it
doesn't change the graphical list of outputs of the tool. How can I fix it?
I want something like the Input, where it shows different outputs according
to the selected parameter from the select.

Here is the XML code:


inputs
param name=input_dataset label=Input dataset (ShoweLab or FBK
Format) to split type=data format=showelab-dataset,fbk-svm-dataset/
conditional name=format_condition

param name=format_options label=Choose the type of dataset
you want to split type=select
option value=fbkFBK Format/option
option value=showelab selected=TrueShoweLab
Format/option
/param
when value=fbk
param name=input_fbk_dataset_labels label=Input dataset
labels (FBK Format) to split type=data format=fbk-labels/
/when
when value=showelab /
/conditional
param name=split_perc label=Percentage of Training Set among
complete dataset type=float min=0.05 max=0.95 value=0.75/
/inputs
outputs
data format=showelab-dataset name=trainingDataset
label=Training Dataset extracted from ${input_dataset.name}
filterformat_condition[format_options] ==
showelab/filter
/data
data format=showelab-dataset name=validationDataset
label=Validation Dataset extracted from ${input_dataset.name}
filterformat_condition[format_options] ==
showelab/filter
/data
data format=fbk-svm-dataset name=trainingDataset
label=Training Dataset extracted from ${input_dataset.name}
filterformat_condition[format_options]  == fbk/filter
/data
data format=fbk-labels name=trainingLabels label=Training
Dataset Labels extracted from ${input_fbk_dataset_labels.name}
filterformat_condition[format_options]  == fbk/filter
/data
data format=fbk-svm-dataset name=validationDataset
label=Validation Dataset extracted from ${input_dataset.name}
filterformat_condition[format_options]  == fbk/filter
/data
data format=fbk-labels name=validationLabels label=Validation
Dataset Labels extracted from ${input_fbk_dataset_labels.name}
filterformat_condition[format_options]  == fbk/filter
/data
/outputs





On Wed, Jul 16, 2014 at 6:54 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:

 On Wed, Jul 16, 2014 at 5:28 PM, Calogero Zarbo za...@fbk.eu wrote:
  Hello to everybody
 
  I'm developing my own tool that need to switch the numbers of output
 files
  according to a parameter selected by the user from a list in the inputs
  tag.
  How can I do such thing?
 
  Here is the XML code:
  inputs
  param name=input_dataset label=Input dataset type=data
  format=showelab-dataset,fbk-svm-dataset/
  conditional name=format_condition
 
  param name=format_options label=Choose the type of
 dataset
  you want to split type=select
  option value=fbk.fbk-svm-dataset Format/option
  option value=showelab
 selected=True.showelab-dataset
  Format/option
  /param
  when value=fbk
  param name=input_fbk_dataset_labels label=Input
 dataset
  labels type=data format=fbk-labels/
  /when
  /conditional
 
  /inputs
  outputs
  data format=showelab-dataset name=trainingDataset
  label=Training Dataset extracted from ${input_dataset.name}
  filterformat_options == showelab/filter
  /data
  data format=showelab-dataset name=validationDataset
  label=Validation Dataset extracted from ${input_dataset.name}
  filterformat_options == showelab/filter
  /data
  data format=fbk-svm-dataset name=trainingDataset
  label=Training Dataset extracted from ${input_dataset.name}
  filterformat_options == fbk/filter
  /data
  data format=fbk-labels name=trainingLabels label=Training
  Dataset Labels extracted from ${input_fbk_dataset_labels.name}
  filterformat_options == fbk/filter
  /data
  data format=fbk-svm-dataset name=validationDataset
  label=Validation Dataset extracted from ${input_dataset.name}
  filterformat_options == fbk/filter
  /data
  data format=fbk-labels name=validationLabels
 label=Validation
  Dataset Labels extracted from ${input_fbk_dataset_labels.name}
  filterformat_options == fbk/filter
  /data
 
  /outputs
 
 
  Basically I would like to have in the Workflow Canvas that the outputs
  displayed in the interface will change according to the format_options
  select parameter.
 
  Thanks in advance.

 Hi Calogero,

 I think this tool of mine would serve as a working example:
 

Re: [galaxy-dev] Multiple output tools in Workflow

[Peter Cock]

On Thu, Jul 17, 2014 at 1:58 PM, Calogero Zarbo za...@fbk.eu wrote:
 Hello Peter,

 Thanks for your answer.

 I tried your come but I am still not able to make it work the way I want.
 I mean that in the workflow design page, when I switch the parameter, it
 doesn't change the graphical list of outputs of the tool. How can I fix it?
 I want something like the Input, where it shows different outputs according
 to the selected parameter from the select.

 Here is the XML code:


 inputs
 param name=input_dataset label=Input dataset (ShoweLab or FBK
 Format) to split type=data format=showelab-dataset,fbk-svm-dataset/

 conditional name=format_condition

 param name=format_options label=Choose the type of dataset
 you want to split type=select
 option value=fbkFBK Format/option
 option value=showelab selected=TrueShoweLab
 Format/option
 /param
 when value=fbk
 param name=input_fbk_dataset_labels label=Input dataset
 labels (FBK Format) to split type=data format=fbk-labels/
 /when
 when value=showelab /
 /conditional
 param name=split_perc label=Percentage of Training Set among
 complete dataset type=float min=0.05 max=0.95 value=0.75/

 /inputs
 outputs
 data format=showelab-dataset name=trainingDataset
 label=Training Dataset extracted from ${input_dataset.name}
 filterformat_condition[format_options] ==
 showelab/filter

 /data
 data format=showelab-dataset name=validationDataset
 label=Validation Dataset extracted from ${input_dataset.name}
 filterformat_condition[format_options] ==
 showelab/filter

 /data
 data format=fbk-svm-dataset name=trainingDataset
 label=Training Dataset extracted from ${input_dataset.name}
 filterformat_condition[format_options]  == fbk/filter

 /data
 data format=fbk-labels name=trainingLabels label=Training
 Dataset Labels extracted from ${input_fbk_dataset_labels.name}
 filterformat_condition[format_options]  == fbk/filter

 /data
 data format=fbk-svm-dataset name=validationDataset
 label=Validation Dataset extracted from ${input_dataset.name}
 filterformat_condition[format_options]  == fbk/filter

 /data
 data format=fbk-labels name=validationLabels label=Validation
 Dataset Labels extracted from ${input_fbk_dataset_labels.name}
 filterformat_condition[format_options]  == fbk/filter
 /data
 /outputs

You appear to have multiple defined datasets (three versions of
trainingDataset) which may be the problem, as the name is meant
to be unique.

I think you should have ONE data tag for trainingDataset but
set this up to switch output formats accordingly.

Peter
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Re: [galaxy-dev] Multiple output tools in Workflow

[Calogero Zarbo]

Ok, thanks for the the tip.

I changed the XML to this one:

outputs
data format=showelab-dataset name=trainingDataset
label=Training Dataset extracted from ${input_dataset.name}
change_format
   when input=format_options value=fbk
format=fbk-svm-dataset/
/change_format

/data
data format=showelab-dataset name=validationDataset
label=Validation Dataset extracted from ${input_dataset.name}
change_format
   when input=format_options value=fbk
format=fbk-svm-dataset/
/change_format

/data

data format=fbk-labels name=trainingLabels label=Training
Dataset Labels extracted from ${input_fbk_dataset_labels.name}
filterformat_condition['format_options']  == fbk/filter
/data

data format=fbk-labels name=validationLabels label=Validation
Dataset Labels extracted from ${input_fbk_dataset_labels.name}
filterformat_condition['format_options']  == fbk/filter
/data

/outputs

Still is not working, maybe the when input=format_options value=fbk
format=fbk-svm-dataset/ . Maybe it has some problem since the
format_options parameter is inside a conditional tag?

Thanks a lot for your time.



On Thu, Jul 17, 2014 at 3:08 PM, Peter Cock p.j.a.c...@googlemail.com
wrote:

 On Thu, Jul 17, 2014 at 1:58 PM, Calogero Zarbo za...@fbk.eu wrote:
  Hello Peter,
 
  Thanks for your answer.
 
  I tried your come but I am still not able to make it work the way I want.
  I mean that in the workflow design page, when I switch the parameter, it
  doesn't change the graphical list of outputs of the tool. How can I fix
 it?
  I want something like the Input, where it shows different outputs
 according
  to the selected parameter from the select.
 
  Here is the XML code:
 
 
  inputs
  param name=input_dataset label=Input dataset (ShoweLab or FBK
  Format) to split type=data format=showelab-dataset,fbk-svm-dataset/
 
  conditional name=format_condition
 
  param name=format_options label=Choose the type of
 dataset
  you want to split type=select
  option value=fbkFBK Format/option
  option value=showelab selected=TrueShoweLab
  Format/option
  /param
  when value=fbk
  param name=input_fbk_dataset_labels label=Input
 dataset
  labels (FBK Format) to split type=data format=fbk-labels/
  /when
  when value=showelab /
  /conditional
  param name=split_perc label=Percentage of Training Set among
  complete dataset type=float min=0.05 max=0.95 value=0.75/
 
  /inputs
  outputs
  data format=showelab-dataset name=trainingDataset
  label=Training Dataset extracted from ${input_dataset.name}
  filterformat_condition[format_options] ==
  showelab/filter
 
  /data
  data format=showelab-dataset name=validationDataset
  label=Validation Dataset extracted from ${input_dataset.name}
  filterformat_condition[format_options] ==
  showelab/filter
 
  /data
  data format=fbk-svm-dataset name=trainingDataset
  label=Training Dataset extracted from ${input_dataset.name}
  filterformat_condition[format_options]  == fbk/filter
 
  /data
  data format=fbk-labels name=trainingLabels label=Training
  Dataset Labels extracted from ${input_fbk_dataset_labels.name}
  filterformat_condition[format_options]  == fbk/filter
 
  /data
  data format=fbk-svm-dataset name=validationDataset
  label=Validation Dataset extracted from ${input_dataset.name}
  filterformat_condition[format_options]  == fbk/filter
 
  /data
  data format=fbk-labels name=validationLabels
 label=Validation
  Dataset Labels extracted from ${input_fbk_dataset_labels.name}
  filterformat_condition[format_options]  == fbk/filter
  /data
  /outputs

 You appear to have multiple defined datasets (three versions of
 trainingDataset) which may be the problem, as the name is meant
 to be unique.

 I think you should have ONE data tag for trainingDataset but
 set this up to switch output formats accordingly.

 Peter




-- 
Calogero Zarbo


FBK - Fondazione Bruno Kessler
Center for Information Technology
Mpba - Predictive Models for Biomedicine  Environment
Via Sommarive, 18- 38123 Povo (Trento) IT
e-mail: za...@fbk.eu
https://webmail.fbk.eu/owa/redir.aspx?C=648442797b254191ab144726f9a535e7URL=mailto%3Adefilippi%40fbk.eu
phone: +39 0461 314 674
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Re: [galaxy-dev] Multiple output tools in Workflow

[Peter Cock]

On Thu, Jul 17, 2014 at 2:43 PM, Calogero Zarbo za...@fbk.eu wrote:
 Ok, thanks for the the tip.

 I changed the XML to this one:


 outputs
 data format=showelab-dataset name=trainingDataset
 label=Training Dataset extracted from ${input_dataset.name}
 change_format
when input=format_options value=fbk
 format=fbk-svm-dataset/
 /change_format


 /data
 data format=showelab-dataset name=validationDataset
 label=Validation Dataset extracted from ${input_dataset.name}
 change_format
when input=format_options value=fbk
 format=fbk-svm-dataset/
 /change_format


 /data

 data format=fbk-labels name=trainingLabels label=Training
 Dataset Labels extracted from ${input_fbk_dataset_labels.name}
 filterformat_condition['format_options']  == fbk/filter
 /data

 data format=fbk-labels name=validationLabels label=Validation
 Dataset Labels extracted from ${input_fbk_dataset_labels.name}
 filterformat_condition['format_options']  == fbk/filter
 /data

 /outputs

 Still is not working, maybe the when input=format_options value=fbk
 format=fbk-svm-dataset/ . Maybe it has some problem since the
 format_options parameter is inside a conditional tag?

 Thanks a lot for your time.

I'm not sure off hand - is your complete wrapper in a public repository
somewhere we can look at? However, my general advice would be:

First of all, get it working in the normal tool usage mode (tested by hand).

Then I would get it working with functional tests.

Finally I would test it by hand in the workflow editor, at which point any
problem is probably Galaxy's fault ;)

Peter
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[galaxy-dev] Multiple output tools in Workflow

[Calogero Zarbo]

Hello to everybody

I'm developing my own tool that need to switch the numbers of output files
according to a parameter selected by the user from a list in the inputs
tag.
How can I do such thing?

Here is the XML code:
inputs
param name=input_dataset label=Input dataset type=data
format=showelab-dataset,fbk-svm-dataset/
conditional name=format_condition

param name=format_options label=Choose the type of dataset
you want to split type=select
option value=fbk.fbk-svm-dataset Format/option
option value=showelab
selected=True.showelab-dataset Format/option
/param
when value=fbk
param name=input_fbk_dataset_labels label=Input dataset
labels type=data format=fbk-labels/
/when
/conditional

/inputs
outputs
data format=showelab-dataset name=trainingDataset
label=Training Dataset extracted from ${input_dataset.name}
filterformat_options == showelab/filter
/data
data format=showelab-dataset name=validationDataset
label=Validation Dataset extracted from ${input_dataset.name}
filterformat_options == showelab/filter
/data
data format=fbk-svm-dataset name=trainingDataset
label=Training Dataset extracted from ${input_dataset.name}
filterformat_options == fbk/filter
/data
data format=fbk-labels name=trainingLabels label=Training
Dataset Labels extracted from ${input_fbk_dataset_labels.name}
filterformat_options == fbk/filter
/data
data format=fbk-svm-dataset name=validationDataset
label=Validation Dataset extracted from ${input_dataset.name}
filterformat_options == fbk/filter
/data
data format=fbk-labels name=validationLabels label=Validation
Dataset Labels extracted from ${input_fbk_dataset_labels.name}
filterformat_options == fbk/filter
/data

/outputs


Basically I would like to have in the Workflow Canvas that the outputs
displayed in the interface will change according to the format_options
select parameter.

Thanks in advance.




-- 
Calogero Zarbo


FBK - Fondazione Bruno Kessler
Center for Information Technology
Mpba - Predictive Models for Biomedicine  Environment
Via Sommarive, 18- 38123 Povo (Trento) IT
e-mail: za...@fbk.eu
https://webmail.fbk.eu/owa/redir.aspx?C=648442797b254191ab144726f9a535e7URL=mailto%3Adefilippi%40fbk.eu
phone: +39 0461 314 674
___
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 output tools in Workflow

[Peter Cock]

On Wed, Jul 16, 2014 at 5:28 PM, Calogero Zarbo za...@fbk.eu wrote:
 Hello to everybody

 I'm developing my own tool that need to switch the numbers of output files
 according to a parameter selected by the user from a list in the inputs
 tag.
 How can I do such thing?

 Here is the XML code:
 inputs
 param name=input_dataset label=Input dataset type=data
 format=showelab-dataset,fbk-svm-dataset/
 conditional name=format_condition

 param name=format_options label=Choose the type of dataset
 you want to split type=select
 option value=fbk.fbk-svm-dataset Format/option
 option value=showelab selected=True.showelab-dataset
 Format/option
 /param
 when value=fbk
 param name=input_fbk_dataset_labels label=Input dataset
 labels type=data format=fbk-labels/
 /when
 /conditional

 /inputs
 outputs
 data format=showelab-dataset name=trainingDataset
 label=Training Dataset extracted from ${input_dataset.name}
 filterformat_options == showelab/filter
 /data
 data format=showelab-dataset name=validationDataset
 label=Validation Dataset extracted from ${input_dataset.name}
 filterformat_options == showelab/filter
 /data
 data format=fbk-svm-dataset name=trainingDataset
 label=Training Dataset extracted from ${input_dataset.name}
 filterformat_options == fbk/filter
 /data
 data format=fbk-labels name=trainingLabels label=Training
 Dataset Labels extracted from ${input_fbk_dataset_labels.name}
 filterformat_options == fbk/filter
 /data
 data format=fbk-svm-dataset name=validationDataset
 label=Validation Dataset extracted from ${input_dataset.name}
 filterformat_options == fbk/filter
 /data
 data format=fbk-labels name=validationLabels label=Validation
 Dataset Labels extracted from ${input_fbk_dataset_labels.name}
 filterformat_options == fbk/filter
 /data

 /outputs


 Basically I would like to have in the Workflow Canvas that the outputs
 displayed in the interface will change according to the format_options
 select parameter.

 Thanks in advance.

Hi Calogero,

I think this tool of mine would serve as a working example:
https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id

Peter
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