CLI typo fix

mikessh · Jul 21, 2015 · 1743ca5 · 1743ca5
1 parent d0b65e5
commit 1743ca5
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Showing 12 changed files with 12 additions and 12 deletions.
diff --git a/src/main/groovy/com/antigenomics/vdjtools/basic/CalcSegmentUsage.groovy b/src/main/groovy/com/antigenomics/vdjtools/basic/CalcSegmentUsage.groovy
@@ -30,7 +30,7 @@ cli.m(longOpt: "metadata", argName: "filename", args: 1,
         "Metadata file. First and second columns should contain file name and sample id. " +
                 "Header is mandatory and will be used to assign column names for metadata.")
 cli.u(longOpt: "unweighted", "Will count each clonotype only once, apart from conventional frequency-weighted histogram.")
-cli._(longOpt: "plot-type", argName: "<pdf|png>", args: 1, "Plot output format [default=pdf]")
+cli._(longOpt: "plot-type", argName: "pdf|png", args: 1, "Plot output format [default=pdf]")
 cli.p(longOpt: "plot", "Plot V/J usage heatmaps and perform cluster analysis")
 cli.n(longOpt: "num-factor", "Numeric factor variable")
 cli.l(longOpt: "label", argName: "string", args: 1, "Metadata entry used to annotate the heatmap")

diff --git a/src/main/groovy/com/antigenomics/vdjtools/basic/PlotFancySpectratype.groovy b/src/main/groovy/com/antigenomics/vdjtools/basic/PlotFancySpectratype.groovy
@@ -27,7 +27,7 @@ def cli = new CliBuilder(usage: "PlotFancySpectratype [options] input_name outpu
 cli.h("display help message")
 cli.t(longOpt: "top", args: 1, "Number of top clonotypes to present on the histogram. " +
         "Values > $TOP_MAX are not allowed, as they would make the plot legend unreadable. [default = $TOP_DEFAULT]")
-cli._(longOpt: "plot-type", argName: "<pdf|png>", args: 1, "Plot output format [default=pdf]")
+cli._(longOpt: "plot-type", argName: "pdf|png", args: 1, "Plot output format [default=pdf]")
 
 def opt = cli.parse(args)
 

diff --git a/src/main/groovy/com/antigenomics/vdjtools/basic/PlotFancyVJUsage.groovy b/src/main/groovy/com/antigenomics/vdjtools/basic/PlotFancyVJUsage.groovy
@@ -25,7 +25,7 @@ import static com.antigenomics.vdjtools.util.ExecUtil.toPlotPath
 def cli = new CliBuilder(usage: "PlotFancyVJUsage [options] input_name output_prefix")
 cli.h("display help message")
 cli.u(longOpt: "unweighted", "Will count each clonotype only once, apart from conventional frequency-weighted histogram.")
-cli._(longOpt: "plot-type", argName: "<pdf|png>", args: 1, "Plot output format [default=pdf]")
+cli._(longOpt: "plot-type", argName: "pdf|png", args: 1, "Plot output format [default=pdf]")
 
 def opt = cli.parse(args)
 

diff --git a/src/main/groovy/com/antigenomics/vdjtools/basic/PlotSpectratypeV.groovy b/src/main/groovy/com/antigenomics/vdjtools/basic/PlotSpectratypeV.groovy
@@ -28,7 +28,7 @@ cli.h("display help message")
 cli.t(longOpt: "top", args: 1, "Number of top V segments to present on the histogram. " +
         "Values > $TOP_MAX are not allowed, as they would make the plot unreadable. [default = $TOP_DEFAULT]")
 cli.u(longOpt: "unweighted", "Will count each clonotype only once, apart from conventional frequency-weighted histogram.")
-cli._(longOpt: "plot-type", argName: "<pdf|png>", args: 1, "Plot output format [default=pdf]")
+cli._(longOpt: "plot-type", argName: "pdf|png", args: 1, "Plot output format [default=pdf]")
 
 def opt = cli.parse(args)
 

diff --git a/src/main/groovy/com/antigenomics/vdjtools/diversity/PlotQuantileStats.groovy b/src/main/groovy/com/antigenomics/vdjtools/diversity/PlotQuantileStats.groovy
@@ -27,7 +27,7 @@ def cli = new CliBuilder(usage: "PlotQuantileStats [options] input_name output_p
 cli.h("display help message")
 cli.t(longOpt: "top", args: 1, "Number of top clonotypes to present on the histogram. " +
         "Values > $TOP_MAX are not allowed, as they would make the plot unreadable. [default = $TOP_DEFAULT]")
-cli._(longOpt: "plot-type", argName: "<pdf|png>", args: 1, "Plot output format [default=pdf]")
+cli._(longOpt: "plot-type", argName: "pdf|png", args: 1, "Plot output format [default=pdf]")
 
 def opt = cli.parse(args)
 

diff --git a/src/main/groovy/com/antigenomics/vdjtools/diversity/RarefactionPlot.groovy b/src/main/groovy/com/antigenomics/vdjtools/diversity/RarefactionPlot.groovy
@@ -45,7 +45,7 @@ cli.s(longOpt: "steps", argName: "int", args: 1, "Number of steps (points) in th
         "(including 0 and the observed diversity). [default=$STEPS_DEFAULT]")
 
 // plotting:
-cli._(longOpt: "plot-type", argName: "<pdf|png>", args: 1, "Plot output format [default=pdf]")
+cli._(longOpt: "plot-type", argName: "pdf|png", args: 1, "Plot output format [default=pdf]")
 cli.p(longOpt: "plot", "[plotting] Unused.")
 cli.l(longOpt: "label", argName: "string", args: 1,
         "[plotting] Name of metadata column which should be used as label")

diff --git a/src/main/groovy/com/antigenomics/vdjtools/operate/JoinSamples.groovy b/src/main/groovy/com/antigenomics/vdjtools/operate/JoinSamples.groovy
@@ -52,7 +52,7 @@ cli.c(longOpt: "compress", "Compress output sample files.")
 
 // Plotting
 
-cli._(longOpt: "plot-type", argName: "<pdf|png>", args: 1, "Plot output format [default=pdf]")
+cli._(longOpt: "plot-type", argName: "pdf|png", args: 1, "Plot output format [default=pdf]")
 cli.p(longOpt: "plot", "[plotting] Turns on plotting.")
 
 def opt = cli.parse(args)

diff --git a/src/main/groovy/com/antigenomics/vdjtools/overlap/CalcPairwiseDistances.groovy b/src/main/groovy/com/antigenomics/vdjtools/overlap/CalcPairwiseDistances.groovy
@@ -36,7 +36,7 @@ cli._(longOpt: "low-mem", "Will process all sample pairs sequentially, avoiding"
 cli.i(longOpt: "intersect-type", argName: "string", args: 1,
         "Intersection rule to apply. Allowed values: $OverlapType.allowedNames. " +
                 "Will use '$I_TYPE_DEFAULT' by default.")
-cli._(longOpt: "plot-type", argName: "<pdf|png>", args: 1, "Plot output format [default=pdf]")
+cli._(longOpt: "plot-type", argName: "pdf|png", args: 1, "Plot output format [default=pdf]")
 cli.p(longOpt: "plot", "[plotting] Turns plotting on.")
 
 def opt = cli.parse(args)

diff --git a/src/main/groovy/com/antigenomics/vdjtools/overlap/ClusterSamples.groovy b/src/main/groovy/com/antigenomics/vdjtools/overlap/ClusterSamples.groovy
@@ -41,7 +41,7 @@ cli.i(longOpt: "intersect-type", argName: "string", args: 1,
 
 // Plotting
 
-cli._(longOpt: "plot-type", argName: "<pdf|png>", args: 1, "Plot output format [default=pdf]")
+cli._(longOpt: "plot-type", argName: "pdf|png", args: 1, "Plot output format [default=pdf]")
 cli.f(longOpt: "factor", argName: "string", args: 1,
         "[plotting] Column name, as in metadata. Factor used to color the plot. [default = no factor]")
 cli.n(longOpt: "num-factor", "[plotting] Factor will be treated as numeric value and gradient plot coloring will be used. " +

diff --git a/src/main/groovy/com/antigenomics/vdjtools/overlap/OverlapPair.groovy b/src/main/groovy/com/antigenomics/vdjtools/overlap/OverlapPair.groovy
@@ -36,7 +36,7 @@ cli.t(longOpt: "top", args: 1, "Number of top clonotypes which will be provided
 cli.p(longOpt: "plot", "Generate a scatterplot to characterize overlapping clonotypes. " +
         "Also generate abundance difference plot if -c option is specified. " +
         "(R installation with ggplot2, grid and gridExtra packages required).")
-cli._(longOpt: "plot-type", argName: "<pdf|png>", args: 1, "Plot output format [default=pdf]")
+cli._(longOpt: "plot-type", argName: "pdf|png", args: 1, "Plot output format [default=pdf]")
 cli.c(longOpt: "compress", "Compress output sample files.")
 cli._(longOpt: "plot-area-v2", "Use alternative stacked area plot.")
 

diff --git a/src/main/groovy/com/antigenomics/vdjtools/overlap/TestClusters.groovy b/src/main/groovy/com/antigenomics/vdjtools/overlap/TestClusters.groovy
@@ -37,7 +37,7 @@ cli.i(longOpt: "intersect-type", argName: "string", args: 1,
                 "Allowed values: $OverlapType.allowedNames. " +
                 "Will use '$I_TYPE_DEFAULT' by default.")
 cli.n(longOpt: "num-factor", "Treat factor as numeric")
-cli._(longOpt: "plot-type", argName: "<pdf|png>", args: 1, "Plot output format [default=pdf]")
+cli._(longOpt: "plot-type", argName: "pdf|png", args: 1, "Plot output format [default=pdf]")
 
 def opt = cli.parse(args)
 

diff --git a/src/main/groovy/com/antigenomics/vdjtools/overlap/TrackClonotypes.groovy b/src/main/groovy/com/antigenomics/vdjtools/overlap/TrackClonotypes.groovy
@@ -61,7 +61,7 @@ cli.s(longOpt: "sequence", argName: "[t1,t2,t3,...]", args: 1,
 cli.f(longOpt: "factor", argName: "string", args: 1,
         "[plotting] Column name, as in metadata. Factor to be treated as time variable. [default = \"time\"]")
 cli.p(longOpt: "plot", "[plotting] Turns on plotting.")
-cli._(longOpt: "plot-type", argName: "<pdf|png>", args: 1, "Plot output format [default=pdf]")
+cli._(longOpt: "plot-type", argName: "pdf|png", args: 1, "Plot output format [default=pdf]")
 
 def opt = cli.parse(args)