Modify the CAP3 dialog

Modify the "Contig Assembly with CAP3" dialog as follows:

1. Rename the dialog to "De Novo Assemble Sanger Reads with CAP3".
2. Rename the first tab inside dialog from "Base" to "General".
3. Remove all current widgets from the "General tab and replace them with the following widgets (see also the "Map Sanger Reads to Reference" dialog):
   • There should be three groups inside the tab: "Input data", "Main settings", "Result alignment".
   • The "Input data" group contains a widget for reads with "Add" and "Remove" buttons. Decrease the vertical size of the reads widget a little bit.
   • The "Main settings" group contains three parameters that should be moved there from the "Advanced" tab of the dialog. That is:
     • "Base quality cutoff for clipping" (the parameter has the same name on the "Advanced" tab).
     • "Min overlap length" (corresponds to "Overlap length cutoff").
     • "Min overlap identity" (corresponds to "Overlap percent identity cutoff"). Also, add "%" into the spin box.
   • The "Result alignment" group should be as in the "Map Sanger Reads to Reference" dialog: an edit box with the browse button, the "Add to project" checkbox. The default name should be "sanger_reads_alignment.ugenedb" (or "sanger_reads_alignment_1.ugenedb", if the previous file exists, etc.). Note: In some scenarios several output files may be produced by CAP3, in this case the same number auto-incremental rules should be applied to the base file name, specified in this field.
4. On the "Advanced" tab:
   • Rename the "Clipping for poor regions" to "Clipping of poor regions".
   • Remove "Base quality cutoff for clipping (-c)" parameter from the group.
   • Add a new parameter "Min number pf good reads at clip position (-z)" to the group (under the "Clipping range (-y)" parameter). The value is an integer number. Min possible value is "1". The default value is "2". Pass "-z VALUE" to the command line launch of the CAP3 external tool.
   • Remove the "Length and percent identity of an overlap" group with both parameters.
   • Rename "Assembly reverse reads" to "Assemble reverse reads".
5. Rename the "Run" button in the dialog to "Assemble".