UGENE Forum - Newbie: Facing problem on CMD Tools

Reply #60 - Mar 2^nd, 2012 at 8:22am

kenkl Offline
Junior Member

Posts: 73

Hi!

May I know how to use the "Multiplexer" element in the snapshot?

Thnaks!

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Reply #61 - Mar 2^nd, 2012 at 4:12pm

kenkl Offline
Junior Member

Posts: 73

Hi, I'm facing problem with one of my custom CMDline tool.

I had written the execution string (see screenshot) but it appears differently when the element is created (see screenshot). It gave an empty output file, suspect that may be due to the absent of '<' sign in the element created.

On top of that I had tried the program in commandline and it works well.

Kindly advice. Thanks!

Kenneth

error_001.png (101 KB | )

blastout.png (19 KB | )

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Reply #62 - Mar 5^th, 2012 at 12:06pm

German Offline
Full Member

Posts: 118

kenkl wrote on Mar 2^nd, 2012 at 8:22am:

Hi!

May I know how to use the "Multiplexer" element in the snapshot?

Thnaks!

Hello!
The multiplexer element is needed to join two separate data flows into the single data flow. But a user should set a rule of data multiplexing.

There are 4 multiplexing rules:
1) 1 to 1 - for each incoming message from one input it waits for only one incoming message from another input and puts the united message to the output.

2) 1 to many - for each incoming message from the first input it waits for only every incoming message from the second input and puts the united messages to the output.

3) Many to 1 - for each incoming message from the second input it waits for only every incoming message from the second input and puts the united messages to the output.

4) Streaming mode - multiplexer transports messages as they are from inputs to the output without joining them.

There is also another parameter "If empty input". Sometimes one of the inputs (working input) receives some data but another input (closed input) becomes closed without providing any data. So, a user should set the behavior of the multiplexer for these situations. There are two variants:
1) Fill by empty values - multiplexer transports every incoming message from the working input to the output despite that the closed input receives nothing. In this case, if some of next elements should receive some data from the channel through the closed input then this element would receive empty values.

2) Truncate - don't put anything to the output if some of inputs becomes closed.

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Reply #63 - Mar 5^th, 2012 at 12:30pm

German Offline
Full Member

Posts: 118

There is also a new feature which is connected with multiplexing.
In some schemes you need to divide the data flow and then to join it back using the multiplexer (see the screenshot).

The separated data could go through the elements which brake the data flow (currently, these elements are only filters).
You can see this situation on the screenshot. The data flow goes through the Filter 1 and Filter 2. So, the inputs of the multiplexer receive two different data sets, because the data flow is broken by filters.
And then these flows are joined to the single flow.

In this case, if you want to connect the sequence slot from "Read sequence" with the sequence slot of "Write sequence", you should set what path the sequence went through. As you can see from the screenshot, there are two sequences: a sequence, that goes through the Filter 1, and a sequences, that goes through the Filter 2.

filters.JPG (55 KB | )

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Reply #64 - Mar 5^th, 2012 at 12:40pm

kenkl Offline
Junior Member

Posts: 73

kenkl wrote on Mar 2^nd, 2012 at 4:12pm:

Hi, I'm facing problem with one of my custom CMDline tool.

I had written the execution string (see screenshot) but it appears differently when the element is created (see screenshot). It gave an empty output file, suspect that may be due to the absent of '<' sign in the element created.

On top of that I had tried the program in commandline and it works well.

Kindly advice. Thanks!

Kenneth

Hi German, how about this issue above yea?

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Reply #65 - Mar 5^th, 2012 at 1:01pm

German Offline
Full Member

Posts: 118

kenkl wrote on Mar 2^nd, 2012 at 4:12pm:

Hi, I'm facing problem with one of my custom CMDline tool.

I had written the execution string (see screenshot) but it appears differently when the element is created (see screenshot). It gave an empty output file, suspect that may be due to the absent of '<' sign in the element created.

On top of that I had tried the program in commandline and it works well.

Kindly advice. Thanks!

Kenneth

The problem appears because the stdin redirection ("<") is not implemented in WD. Currently, I can't answer you why ">" is implemented well, but "<" is not. Maybe there are some complex problems connected with this issue.

We will investigate it asap and tell you about the results. The corresponded issue is created:
https://ugene.unipro.ru/tracker/browse/UGENE-867

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Reply #66 - Mar 12^th, 2012 at 10:55am

kenkl Offline
Junior Member

Posts: 73

Hi! I'm just wondering is it possible that user could combine 2 programs in one single custom CMDline element. For instance ttuner that has 2 function, base calling and producing quality score. Instead of creating 2 elements can i incorporate it into the custom CMDline? Just curious on this.

Kenneth

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Reply #67 - Mar 13^th, 2012 at 12:45pm

German Offline
Full Member

Posts: 118

kenkl wrote on Mar 12^th, 2012 at 10:55am:

Hi! I'm just wondering is it possible that user could combine 2 programs in one single custom CMDline element. For instance ttuner that has 2 function, base calling and producing quality score. Instead of creating 2 elements can i incorporate it into the custom CMDline? Just curious on this.

Kenneth

Could you describe the problem in details? It is not so understandable what is "combine 2 programs in one element".
Describe, please, how do you want to combine programs? Or what should this element do?

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Reply #68 - Mar 13^th, 2012 at 2:44pm

kenkl Offline
Junior Member

Posts: 73

Hi, thanks for replying. This inquiry arise due to the function of one tools: ttuner.

At present, I need to create 2 custom CMDline elements for ttuner, 1 for base calling, the other 1 for calling quality values. So instead of creating 2 element for those 2 functions, is it possible that I can put a semi-colon ( Wink

for this purpose?

E.g:
ttuner -sa $infile $outfile ; ttuner -qa $infile $outfile

with the above in the execution string in a single custom CMDline element? Though I can do it with 2 elements but just an idea not sure whether this would work or not. Thanks!

Kenneth

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Reply #69 - Mar 15^th, 2012 at 1:17pm

German Offline
Full Member

Posts: 118

kenkl wrote on Mar 13^th, 2012 at 2:44pm:

Hi, thanks for replying. This inquiry arise due to the function of one tools: ttuner.

At present, I need to create 2 custom CMDline elements for ttuner, 1 for base calling, the other 1 for calling quality values. So instead of creating 2 element for those 2 functions, is it possible that I can put a semi-colon ( Wink

for this purpose?

E.g:
ttuner -sa $infile $outfile ; ttuner -qa $infile $outfile

with the above in the execution string in a single custom CMDline element? Though I can do it with 2 elements but just an idea not sure whether this would work or not. Thanks!

Kenneth

We will think about that. Thanks for your ideas, Kenneth.

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Reply #70 - Apr 18^th, 2012 at 8:58am

kenkl Offline
Junior Member

Posts: 73

German wrote on Mar 5^th, 2012 at 12:30pm:

There is also a new feature which is connected with multiplexing.
In some schemes you need to divide the data flow and then to join it back using the multiplexer (see the screenshot).

The separated data could go through the elements which brake the data flow (currently, these elements are only filters).
You can see this situation on the screenshot. The data flow goes through the Filter 1 and Filter 2. So, the inputs of the multiplexer receive two different data sets, because the data flow is broken by filters.
And then these flows are joined to the single flow.

In this case, if you want to connect the sequence slot from "Read sequence" with the sequence slot of "Write sequence", you should set what path the sequence went through. As you can see from the screenshot, there are two sequences: a sequence, that goes through the Filter 1, and a sequences, that goes through the Filter 2.

Hi German,

May I know how to use the Filter element and the Sequence Marker element? I'm trying to mark and filter out Blast results with certain identity threshold. Thanks!

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Reply #71 - Apr 18^th, 2012 at 1:48pm

German Offline
Full Member

Posts: 118

All information about sequence markers and filters is available in our documentation:
http://ugene.unipro.ru/documentation/wd_manual/workflow_elements/data_flow/marke...
http://ugene.unipro.ru/documentation/wd_manual/workflow_elements/data_flow/filte...

You can set up a new marker group to the sequence marker. And the corresponding output text slot will be added to the sequence marker.

The data provided by this slot could be used at the filter element. You just need to bind the marker group slot with filter input slot; and set the "Filter by value(s)" parameter as you wish.

For example, if you set up the marker that values of the marker group are "good" and "bad" (and "rest" for unmarked data) then the "Filter by value(s)" parameter could be set as "good", or "bad", or "rest" (or comma separated values: "good, rest").

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