Support plink --const-fid argument

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/PlinkPcaStep.java

@@ -41,6 +41,9 @@ public Provider()
                     ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--not-chr"), "excludedContigs", "Excluded Contigs", "A comma separated list of contigs to exclude, such as X,Y,MT.", "textfield", new JSONObject(){{
 
                     }}, "X,Y,MT"),
+                    ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--const-fid"), "constFid", "Constant FID", "Converts sample IDs to within-family IDs while setting all family IDs to a single value (default '0').", "checkbox", new JSONObject(){{
+                        put("checked", true);
+                    }}, true),
                     ToolParameterDescriptor.create(SelectSamplesStep.SAMPLE_INCLUDE, "Sample(s) Include", "Only the following samples will be included in the analysis.", "sequenceanalysis-trimmingtextarea", null, null),
                     ToolParameterDescriptor.create(SelectSamplesStep.SAMPLE_EXCLUDE, "Samples(s) To Exclude", "The following samples will be excluded from the analysis.", "sequenceanalysis-trimmingtextarea", null, null)
             ), Arrays.asList("sequenceanalysis/field/TrimmingTextArea.js"), "https://zzz.bwh.harvard.edu/plink/");