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Format -help CLI option

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efischer
2022-02-27 16:53:46 -06:00
parent 12b003a69f
commit b1155f8100
1 changed files with 13 additions and 17 deletions
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30
src/main/java/CommandLineInterface.java
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@@ -197,7 +197,9 @@ public class CommandLineInterface {
private static Options buildMainOptions() { private static Options buildMainOptions() {
Options mainOptions = new Options(); Options mainOptions = new Options();
Option help = Option.builder("help").build(); Option help = Option.builder("help")
.desc("Displays this help menu")
.build();
Option makeCells = Option.builder("cells") Option makeCells = Option.builder("cells")
.longOpt("make-cells") .longOpt("make-cells")
.desc("Makes a cell sample file of distinct T cells") .desc("Makes a cell sample file of distinct T cells")
@@ -292,21 +294,19 @@ public class CommandLineInterface {
OptionGroup wellPopOptions = new OptionGroup(); // add this to plate options OptionGroup wellPopOptions = new OptionGroup(); // add this to plate options
wellPopOptions.setRequired(true); wellPopOptions.setRequired(true);
Option randomWellPopulations = Option.builder("random") Option randomWellPopulations = Option.builder("random")
.desc("Randomize well populations on sample plate.") .desc("Randomize well populations on sample plate. Takes two arguments: the minimum possible population and the maximum possible population.")
.hasArgs() .hasArgs()
.numberOfArgs(2) .numberOfArgs(2)
.argName("max_pop min_pop") .argName("minimum maximum")
.build(); .build();
Option specificWellPopulations = Option.builder("pop") Option specificWellPopulations = Option.builder("pop")
.longOpt("populations") .desc("The well populations for each section of the sample plate. There will be as many sections as there are populations given.")
.desc("The well populations for each section of the sample plate. There will be as many sections as populations given.")
.hasArgs() .hasArgs()
.argName("1st_pop [2nd_pop]...") .argName("number [number]...")
.build(); .build();
Option dropoutRate = Option.builder("err") //add this to plate options Option dropoutRate = Option.builder("err") //add this to plate options
.longOpt("dropout-rate")
.hasArg() .hasArg()
.desc("The sequence dropout rate due to amplification error") .desc("The sequence dropout rate due to amplification error. (0.0 - 1.0)")
.argName("rate") .argName("rate")
.required() .required()
.build(); .build();
@@ -355,33 +355,29 @@ public class CommandLineInterface {
Options matchCDR3options = new Options(); Options matchCDR3options = new Options();
Option graphFilename = Option.builder("g") Option graphFilename = Option.builder("g")
.longOpt("graph-file") .longOpt("graph-file")
.desc("Graph/data file to use") .desc("The graph/data file to use")
.hasArg() .hasArg()
.argName("filename") .argName("filename")
.required().build(); .required().build();
Option minOccupancyOverlap = Option.builder("min") Option minOccupancyOverlap = Option.builder("min")
.longOpt("min-overlap-size")
.desc("The minimum number of shared wells to attempt to match a sequence pair") .desc("The minimum number of shared wells to attempt to match a sequence pair")
.hasArg() .hasArg()
.argName("minimum") .argName("number")
.required().build(); .required().build();
Option maxOccupancyOverlap = Option.builder("max") Option maxOccupancyOverlap = Option.builder("max")
.longOpt("max_overlap_size")
.desc("The maximum number of shared wells to attempt to match a sequence pair") .desc("The maximum number of shared wells to attempt to match a sequence pair")
.hasArg() .hasArg()
.argName("maximum") .argName("number")
.required().build(); .required().build();
Option minOverlapPercent = Option.builder("minpct") Option minOverlapPercent = Option.builder("minpct")
.longOpt("min-overlap-percent")
.desc("(Optional) The minimum percentage of a sequence's total occupancy shared by another sequence to attempt matching. (0 - 100) ") .desc("(Optional) The minimum percentage of a sequence's total occupancy shared by another sequence to attempt matching. (0 - 100) ")
.hasArg() .hasArg()
.argName("minimum") .argName("percent")
.build(); .build();
Option maxOccupancyDifference = Option.builder("maxdiff") Option maxOccupancyDifference = Option.builder("maxdiff")
.longOpt("max-occupancy-difference")
.desc("(Optional) The maximum difference in total occupancy between two sequences to attempt matching.") .desc("(Optional) The maximum difference in total occupancy between two sequences to attempt matching.")
.hasArg() .hasArg()
.argName("maximum") .argName("number")
.build(); .build();
matchCDR3options.addOption(graphFilename); matchCDR3options.addOption(graphFilename);
matchCDR3options.addOption(minOccupancyOverlap); matchCDR3options.addOption(minOccupancyOverlap);