Fix subject filter in RenameSamplesForMgapStep

Author: bbimber

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

@@ -60,6 +60,9 @@ public Provider()
                     ToolParameterDescriptor.createCommandLineParam(CommandLineParam.createSwitch("--remove-unused-alternates"), "trimAlternates", "Remove Unused Alternates", "If selected, any alternate alleles not used in any genotypes will be trimmed.", "checkbox", null, null),
                     ToolParameterDescriptor.createCommandLineParam(CommandLineParam.createSwitch("--sites-only-vcf-output"), "sitesOnly", "Sites Only VCF Output", "If selected, the resulting VCF will omit samples and include only the site information.", "checkbox", null, null),
                     ToolParameterDescriptor.createCommandLineParam(CommandLineParam.createSwitch("--allow-nonoverlapping-command-line-samples"), "allowNnonoverlappingSamples", "Allow non-overlapping Samples", "Normally the job will fail is samples are selected that do not exist in the VCF.  If checked, this will be allowed.", "checkbox", null, null),
+                    ToolParameterDescriptor.createCommandLineParam(CommandLineParam.createSwitch("--set-filtered-gt-to-nocall"), "setFilteredGtToNocall", "Set Filtered Genotypes to No-Call", "If selected, any filtered genotypes will be converted to no-call.", "checkbox", new JSONObject(){{
+                        put("checked", true);
+                    }}, true),
                     ToolParameterDescriptor.create(SELECT_TYPE_TO_INCLUDE, "Select Type(s) To Include", "Only variants of the selected type(s) will be included", "ldk-simplecombo", new JSONObject(){{
                         put("storeValues", SelectSNVsStep.getSelectTypes());
                         put("multiSelect", true);
@@ -70,10 +73,7 @@ public Provider()
                     }}, null),
                     new IntervalParameterDescriptor(),
                     ToolParameterDescriptor.create(SelectSamplesStep.SAMPLE_INCLUDE, "Select Sample(s) Include", "Only variants of the selected type(s) will be included", "sequenceanalysis-trimmingtextarea", null, null),
-                    ToolParameterDescriptor.create(SelectSamplesStep.SAMPLE_EXCLUDE, "Select Samples(s) To Exclude", "Variants of the selected type(s) will be excluded", "sequenceanalysis-trimmingtextarea", null, null),
-                    ToolParameterDescriptor.createCommandLineParam(CommandLineParam.createSwitch("--set-filtered-gt-to-nocall"), "setFilteredGtToNocall", "Set Filtered Genotypes to No-Call", "If selected, any filtered genotypes will be converted to no-call.", "checkbox", new JSONObject(){{
-                        put("checked", true);
-                    }}, true)
+                    ToolParameterDescriptor.create(SelectSamplesStep.SAMPLE_EXCLUDE, "Select Samples(s) To Exclude", "Variants of the selected type(s) will be excluded", "sequenceanalysis-trimmingtextarea", null, null)
             ), Arrays.asList("sequenceanalysis/panel/VariantFilterPanel.js", "sequenceanalysis/panel/IntervalPanel.js", "/sequenceanalysis/field/TrimmingTextArea.js"), "");
         }