Automating running command on Linux from Windows using PuTTY

I have a scenario where I need to run a linux shell command frequently (with different filenames) from windows. I am using PuTTY and WinSCP to do that (requires login name and password). The file is copied to a predefined folder in the linux machine through WinSCP and then the command is run from PuTTY. Is there a way by which I can automate this through a program. Ideally I would like to right click the file from windows and issue the command which would copy the file to remote machine and run the predefined command (in PuTTy) with the filename as argument.

Putty usually comes with the "plink" utility.
This is essentially the "ssh" command line command implemented as a windows .exe.
It pretty well documented in the putty manual under "Using the command line tool plink".

You just need to wrap a command like:

plink root@myserver /etc/backups/do-backup.sh

in a .bat script.

You can also use common shell constructs, like semicolons to execute multiple commands. e.g:

plink read@myhost ls -lrt /home/read/files;/etc/backups/do-backup.sh

There could be security issues with common methods for auto-login. One of the most easiest ways is documented below:

• Running Putty from the Windows Command Line

And as for the part the executes the command In putty UI, Connection>SSH> there's a field for remote command.

4.17 The SSH panel

The SSH panel allows you to configure options that only apply to SSH sessions.

4.17.1 Executing a specific command on the server

In SSH, you don't have to run a general shell session on the server. Instead, you can choose to run a single specific command (such as a mail user agent, for example). If you want to do this, enter the command in the "Remote command" box. http://the.earth.li/~sgtatham/putty/0.53/htmldoc/Chapter4.html

in short, your answers might just as well be similar to the text below:

• let Putty run command in remote server

You can write a TCL script and establish SSH session to that Linux machine and issue commands automatically. Check http://wiki.tcl.tk/11542 for a short tutorial.