Re: [galaxy-dev] Workflow Compatibility

[Katherine Beaulieu]

Hi Brad,
So with multiple selection dropdown lists this is possible? Do you have an
example of a tool that can do this? Would it be possible to see an example
of the tools you are talking about? Thanks for the help!
Katherine

On Fri, Aug 26, 2016 at 12:05 PM, Langhorst, Brad  wrote:

> Hi Katherine:
>
> I’d recommend not having users type in paths if at all possible (they will
> make frustrating mistakes).
> If there is a selection of these maybe consider turining them into
> dropdown lists.
>
> Either way,  these would be no different than e.g. user specified
> downsampling  amounts. or library names, etc.
> I have tools that accept many of these.
>
>
> Brad
>
> —
> Brad Langhorst, Ph.D.
> Development Scientist
> New England Biolabs
>
>
>
>
> On Aug 26, 2016, at 10:57 AM, Katherine Beaulieu <
> katherine.beaulieu...@gmail.com> wrote:
>
> What if its multiple file paths that the user types in rather than actual
> files, which makes it so the tool can't be executed in batch mode, would it
> still be workflow compatible at that point? Thanks for pointing me to the
> Bowtie wrappers as an example.
>
>
>
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Re: [galaxy-dev] Workflow Compatibility

[Langhorst, Brad]

Hi Katherine:

I’d recommend not having users type in paths if at all possible (they will make 
frustrating mistakes).
If there is a selection of these maybe consider turining them into dropdown 
lists.

Either way,  these would be no different than e.g. user specified downsampling  
amounts. or library names, etc.
I have tools that accept many of these.


Brad

—
Brad Langhorst, Ph.D.
Development Scientist
New England Biolabs




On Aug 26, 2016, at 10:57 AM, Katherine Beaulieu 
> wrote:

What if its multiple file paths that the user types in rather than actual 
files, which makes it so the tool can't be executed in batch mode, would it 
still be workflow compatible at that point? Thanks for pointing me to the 
Bowtie wrappers as an example.


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Re: [galaxy-dev] Workflow Compatibility

[Katherine Beaulieu]

Hi Brad,
What if its multiple file paths that the user types in rather than actual
files, which makes it so the tool can't be executed in batch mode, would it
still be workflow compatible at that point? Thanks for pointing me to the
Bowtie wrappers as an example.
Katherine

On Fri, Aug 26, 2016 at 10:45 AM, Langhorst, Brad  wrote:

> HI Katherine:
>
> Multi-input/output should work fine…
>
> You could have a look at the bowtie wrappers for an example.
>
> It takes up to 2 fastq files and a reference. I can output a few files
> (unmapped, mapped, etc)
>
>
> Brad
> —
> Brad Langhorst, Ph.D.
> Development Scientist
> New England Biolabs
>
>
>
>
> On Aug 26, 2016, at 10:42 AM, Katherine Beaulieu <
> katherine.beaulieu...@gmail.com> wrote:
>
>
>
> On Fri, Aug 26, 2016 at 10:42 AM, Katherine Beaulieu <
> katherine.beaulieu...@gmail.com> wrote:
>
>> Hi Peter,
>> I think I did not explain myself well. I meant that if I have a tool that
>> takes multiple file paths and outputs multiple Galaxy datasets to the
>> history, would this tool be workflow compatible, meaning capable of being a
>> part of any workflow? From the behaviour I am getting now I am assuming it
>> isn't but I just wanted to confirm that this isn't supported functionality.
>>
>> On Fri, Aug 26, 2016 at 10:34 AM, Peter Cock 
>> wrote:
>>
>>> Hi Katherine,
>>>
>>> Are you asking about compatibility staying on the same Galaxy
>>> instance, or the harder problem of compatibility sharing workflows
>>> between Galaxy servers?
>>>
>>> Taking data from input Galaxy datasets should be fine, anything else
>>> may not be portable. Even the relatively simple case of using
>>> datafiles referenced via an example.loc file (e.g. BLAST databases)
>>> would require the entries in the example.loc file be synchronised
>>> between Galaxy instances, and the associated data files too.
>>>
>>> Peter
>>>
>>>
>>> On Fri, Aug 26, 2016 at 1:27 PM, Katherine Beaulieu
>>>  wrote:
>>> > Hi Everyone,
>>> > Would anyone be able to tell me the conditions which would make a tool
>>> > non-workflow compatible? I have a tool that imports files from a third
>>> party
>>> > application and auto-detects the file format. There is also the option
>>> to
>>> > upload multiple files at once so the tool always uploads at least two
>>> files.
>>> > From what I have described can anyone see why this tool would not be
>>> able to
>>> > send one of its files to the next tool in the chain, ex. a text
>>> manipulation
>>> > tool?
>>> > Thanks,
>>> > Katherine
>>> >
>>> > ___
>>> > 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:
>>> >   https://lists.galaxyproject.org/
>>> >
>>> > To search Galaxy mailing lists use the unified search at:
>>> >   http://galaxyproject.org/search/mailinglists/
>>>
>>
>>
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Re: [galaxy-dev] Workflow Compatibility

[Katherine Beaulieu]

On Fri, Aug 26, 2016 at 10:42 AM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:

> Hi Peter,
> I think I did not explain myself well. I meant that if I have a tool that
> takes multiple file paths and outputs multiple Galaxy datasets to the
> history, would this tool be workflow compatible, meaning capable of being a
> part of any workflow? From the behaviour I am getting now I am assuming it
> isn't but I just wanted to confirm that this isn't supported functionality.
>
> On Fri, Aug 26, 2016 at 10:34 AM, Peter Cock 
> wrote:
>
>> Hi Katherine,
>>
>> Are you asking about compatibility staying on the same Galaxy
>> instance, or the harder problem of compatibility sharing workflows
>> between Galaxy servers?
>>
>> Taking data from input Galaxy datasets should be fine, anything else
>> may not be portable. Even the relatively simple case of using
>> datafiles referenced via an example.loc file (e.g. BLAST databases)
>> would require the entries in the example.loc file be synchronised
>> between Galaxy instances, and the associated data files too.
>>
>> Peter
>>
>>
>> On Fri, Aug 26, 2016 at 1:27 PM, Katherine Beaulieu
>>  wrote:
>> > Hi Everyone,
>> > Would anyone be able to tell me the conditions which would make a tool
>> > non-workflow compatible? I have a tool that imports files from a third
>> party
>> > application and auto-detects the file format. There is also the option
>> to
>> > upload multiple files at once so the tool always uploads at least two
>> files.
>> > From what I have described can anyone see why this tool would not be
>> able to
>> > send one of its files to the next tool in the chain, ex. a text
>> manipulation
>> > tool?
>> > Thanks,
>> > Katherine
>> >
>> > ___
>> > 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:
>> >   https://lists.galaxyproject.org/
>> >
>> > To search Galaxy mailing lists use the unified search at:
>> >   http://galaxyproject.org/search/mailinglists/
>>
>
>
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Re: [galaxy-dev] Workflow Compatibility

[Peter Cock]

Hi Katherine,

Are you asking about compatibility staying on the same Galaxy
instance, or the harder problem of compatibility sharing workflows
between Galaxy servers?

Taking data from input Galaxy datasets should be fine, anything else
may not be portable. Even the relatively simple case of using
datafiles referenced via an example.loc file (e.g. BLAST databases)
would require the entries in the example.loc file be synchronised
between Galaxy instances, and the associated data files too.

Peter


On Fri, Aug 26, 2016 at 1:27 PM, Katherine Beaulieu
 wrote:
> Hi Everyone,
> Would anyone be able to tell me the conditions which would make a tool
> non-workflow compatible? I have a tool that imports files from a third party
> application and auto-detects the file format. There is also the option to
> upload multiple files at once so the tool always uploads at least two files.
> From what I have described can anyone see why this tool would not be able to
> send one of its files to the next tool in the chain, ex. a text manipulation
> tool?
> Thanks,
> Katherine
>
> ___
> 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:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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[galaxy-dev] Workflow Compatibility

[Katherine Beaulieu]

Hi Everyone,
Would anyone be able to tell me the conditions which would make a tool
non-workflow compatible? I have a tool that imports files from a third
party application and auto-detects the file format. There is also the
option to upload multiple files at once so the tool always uploads at least
two files. From what I have described can anyone see why this tool would
not be able to send one of its files to the next tool in the chain, ex. a
text manipulation tool?
Thanks,
Katherine
___
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