Learning Objective
You will learn how to use the the seqan::ArgumentParser and the SeqAn build system so that, at the end, a new SeqAn application can be integrated in KNIME easily. After completing this tutorial, you will be able write a new SeqAn application that can be imported into a KNIME Eclipse plugin with a couple of commands.
Difficulty
Basic
Duration
1.5 h
Prerequisites
A First Example, Parsing Command Line Arguments

In this tutorial you will learn how to write a SeqAn app, which can be, easly converted into a KNIME node.

The first part consists of preparing a dummy app such that it can be used in a KNIME workflow and in the second part you are asked to adapt the app such that it becomes a simple quality control tool.

## Using the seqan::ArgumentParser¶

When we add options to the parser using addOption, we pass an ArgParseOption object together with the parser. The ArgumentType of this ArgParseOption object is highly correlated to how the node generated from our application will look like.

The ArgumentType can be one of the following

*STRING:*  Argument is a string.
*INTEGER:* Argument is a signed 32 bit integer.
*INT64:* Argument is a signed 64 bit integer.
*DOUBLE:* Argument is a floating point number stored as double.
*INPUT_FILE:*  Argument is an input file.
*OUTPUT_FILE:* Argument is an output file.
*INPUT_PREFIX:*  Argument is a prefix to input file(s).
*OUTPUT_PREFIX:* Argument is a prefix to output file(s).


Consider the following example application.




While adding an ArgParseOption to your ArgumentParser you should consider the following points.

• KNIME needs to know the input and output ports of a node. Therefore we must specify them using ArgParseArgument::INPUT_FILE or ArgParseArgument::OUTPUT_FILE as can be seen in the example above.
• In addition, KNIME needs to know the valid file endings, which you can specify with setValidValues, which is also shown in the example.

Tip

Later, when building workflows, you can only connect an output-port of a node to the input-port of the next one if only they have a compatible file endings.

• There are special types of input/output ports which are prefixes to a list of files. Such ports are specified using ArgParseArgument::INPUT_PREFIX or ArgParseArgument::OUTPUT_PREFIX. You can only connect an output prefix port to an input prefix port and vise-versa.

## Using the SeqAn build system to generate KNIME nodes¶

If you are using the SeqAn build system you can generate a workflow plugin directory for all the SeqAn apps including your new one using the target prepare_workflow_plugin.

In order for your application to turn into a KNIME node, you should register your app e.g. my_app, by simply adding the line:

set (SEQAN_CTD_EXECUTABLES \${SEQAN_CTD_EXECUTABLES} <my_app> CACHE INTERNAL "")


to the end of the CMakeList.txt file of your application. All applications with this line in their CMakeList.txt file will be included in the generated plugin when building the targetprepare_workflow_plugin.

Tip

If You are not using the SeqAn build system for some reason, but you used the seqan::ArgumentParser as recommended above, you still can generate a CTD file of your application. After building your application and go to the directory containing the executable of your application and run the following.

./seqan_app_name -write-ctd seqan_app_name.ctd


This will give you the CTD file of your command-line tool. Then you can follow Overview section of the tutorial Generating KNIME Nodes to prepare a plugin directory of your application.