| Previous changeset 75:0a17de046de0 (2017-06-19) Next changeset 77:7bd04a4f29df (2017-06-20) |
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Commit message:
Uploaded 20170620 |
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modified:
loadandplot.xml macros.xml plotwithscale.xml testandplot.xml |
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added:
._loadandplot.R ._plotwithscale.R ._testandplot.R test-data/._.DS_Store test-data/input/._Controls_regions.bed test-data/input/._Elements1_regions.bed test-data/input/._Elements2_regions.bed test-data/input/._Elements3_regions.bed test-data/input/._Feature1.bed test-data/input/._Feature2.bed test-data/input/._features.header.bed.txt test-data/input/._regions.header.txt test-data/output_loadandplot/._iwtomics.loadandplot.RData test-data/output_loadandplot/._iwtomics.loadandplot.features.txt test-data/output_loadandplot/._iwtomics.loadandplot.pdf test-data/output_loadandplot/._iwtomics.loadandplot.regions.txt test-data/output_plotwithscale/._iwtomics.plotwithscale.adjustedpvalue.txt test-data/output_plotwithscale/._iwtomics.plotwithscale.iwtomicstestresults.pdf test-data/output_plotwithscale/._iwtomics.plotwithscale.summaryplot.pdf test-data/output_testandplot/._iwtomics.testandplot.RData test-data/output_testandplot/._iwtomics.testandplot.adjustedpvalue.matrix.txt test-data/output_testandplot/._iwtomics.testandplot.iwtomicstestresults.pdf test-data/output_testandplot/._iwtomics.testandplot.selectedfeatures.txt test-data/output_testandplot/._iwtomics.testandplot.summaryplot.pdf test-data/output_testandplot/._iwtomics.testandplot.tests.txt |
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| diff -r 0a17de046de0 -r 7dcc25a1a062 loadandplot.xml --- a/loadandplot.xml Mon Jun 19 12:09:26 2017 -0400 +++ b/loadandplot.xml Tue Jun 20 12:57:03 2017 -0400 |
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| b'@@ -3,7 +3,7 @@\n <macros>\n <import>macros.xml</import>\n </macros>\n- <expand macro="requirements" />\n+ <!--<expand macro="requirements" />-->\n \n <command detect_errors="exit_code">\n <![CDATA[\n@@ -36,28 +36,25 @@\n #if $conditionaltype.smoothing == \'no\':\n alignment="\'${conditionaltype.alignment}\'"\n #elif $conditionaltype.smoothing == \'locpoly\':\n- alignment="\'${conditionaltype.locpolyconditionalscale.alignment}\'"\n- #if $conditionaltype.locpolyconditionalscale.alignment == \'scale\':\n- scale=\'${conditionaltype.locpolyconditionalscale.scalegrid}\'\n- #end if\n bandwidth=\'${conditionaltype.locpolybandwidth}\'\n degree=\'${conditionaltype.locpolydegree}\'\n- fill_gaps=\'${conditionaltype.fillgaps}\'\n+ alignment="\'${conditionaltype.conditionalscale.alignment}\'"\n #elif $conditionaltype.smoothing == \'kernel\':\n- alignment="\'${conditionaltype.kernelconditionalscale.alignment}\'"\n- #if $conditionaltype.kernelconditionalscale.alignment == \'scale\':\n- scale=\'${conditionaltype.kernelconditionalscale.scalegrid}\'\n- #end if\n bandwidth=\'${conditionaltype.kernelbandwidth}\'\n- fill_gaps=\'${conditionaltype.fillgaps}\'\n+ alignment="\'${conditionaltype.conditionalscale.alignment}\'"\n #elif $conditionaltype.smoothing == \'splines\':\n- alignment="\'${conditionaltype.splinesconditionalscale.alignment}\'"\n- #if $conditionaltype.splinesconditionalscale.alignment == \'scale\':\n- scale=\'${conditionaltype.splinesconditionalscale.scalegrid}\'\n- #end if\n degree=\'${conditionaltype.splinesdegree}\'\n dist_knots=\'${conditionaltype.splinesdistknots}\'\n- fill_gaps=\'${conditionaltype.fillgaps}\'\n+ alignment="\'${conditionaltype.conditionalscale.alignment}\'"\n+ #end if\n+\n+ #if $conditionaltype.smoothing != \'no\':\n+ #if $conditionaltype.conditionalscale.alignment == \'scale\':\n+ scale=\'${conditionaltype.conditionalscale.scalegrid}\'\n+ fill_gaps=\'TRUE\'\n+ #else\n+ fill_gaps=\'${conditionaltype.conditionalscale.fillgaps}\'\n+ #end if\n #end if\n \n average=\'${plotres.average}\'\n@@ -104,101 +101,33 @@\n </param>\n <!-- conditional choice: smoothing=no -->\n <when value="no">\n- <param name="alignment" type="select" label="Region alignment" help="">\n- <option value="center">Center - Alignment on the central position</option>\n- <option value="left">Left - Alignment on the starting position</option>\n- <option value="right">Right - Alignment on the ending position</option>\n- </param>\n+ <expand macro="alignment" />\n </when>\n <!-- conditional choice: smoothing=locpoly -->\n <when value="locpoly">\n- <!-- conditional region alignment -->\n- <conditional name="locpolyconditionalscale">\n- <param name="alignment" type="select" label="Region alignment" help="">\n- <option value="center">Center - Alignment on the central position</option>\n- <option value="left">Left - Alignment on the starting position</option>\n- <option value="right">Right - Alignment on the ending position</option>\n- <option value="scale">Scale - Scaling all regions to the same length</option>\n- </param>\n- <when value="scale">\n- <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." />\n- </when>\n- </conditional>\n-\n <param name="locpolybandwidth" type="integer" value="5" min="2" label="Bandwidth for smoothing" help="" />\n <param name="locpolydegree" type="integer" value="3" min="0" label="Degree of local polynomial" help="" />\n-\n- <!-- fill gaps -->\n- <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label='..b'/option>\n- <option value="right">Right - Alignment on the ending position</option>\n- <option value="scale">Scale - Scaling all regions to the same length</option>\n- </param>\n- <when value="scale">\n- <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." />\n- </when>\n- </conditional>\n-\n- <param name="kernelbandwidth" type="integer" value="5" min="2" label="Bandwidth for smoothing" help="" />\n-\n- <!-- fill gaps -->\n- <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />\n+ <expand macro="alignment-s" />\n </when>\n <!-- conditional choice: smoothing=splines -->\n <when value="splines">\n- <!-- conditional region alignment -->\n- <conditional name="splinesconditionalscale">\n- <param name="alignment" type="select" label="Region alignment" help="">\n- <option value="center">Center - Alignment on the central position</option>\n- <option value="left">Left - Alignment on the starting position</option>\n- <option value="right">Right - Alignment on the ending position</option>\n- <option value="scale">Scale - Scaling all regions to the same length</option>\n- </param>\n- <when value="scale">\n- <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." />\n- </when>\n- </conditional>\n-\n <param name="splinesdegree" type="integer" value="3" min="0" label="Degree of B-splines" help="" />\n <param name="splinesdistknots" type="integer" value="10" min="2" label="Distance between nodes (approximate)" help="" />\n-\n- <!-- fill gaps -->\n- <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" />\n+ <!-- conditional region alignment -->\n+ <expand macro="alignment-s" />\n </when>\n </conditional>\n \n <!-- plot IWTomics results -->\n <section name="plotres" title="Plot data" expanded="True">\n- <!-- average -->\n- <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" help="" />\n- <!-- sample size in each position -->\n- <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" help="" />\n- <!-- conditional plot type -->\n- <conditional name="conditionalplottype">\n- <!-- plot type -->\n- <param name="plottype" type="select" label="Plot type" help="">\n- <option value="boxplot">Pointwise quantile curves (boxplot)</option>\n- <option value="curves">Curves (aligned)</option>\n- </param>\n- <!-- conditional choice: plottype=boxplot -->\n- <when value="boxplot">\n- <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">\n- <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />\n- <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />\n- <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />\n- <repeat name="probabilities" title="Probabilities">\n- <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />\n- </repeat>\n- </section>\n- </when>\n- </conditional>\n+ <expand macro="plot-params" />\n </section>\n </inputs>\n \n' |
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| diff -r 0a17de046de0 -r 7dcc25a1a062 macros.xml --- a/macros.xml Mon Jun 19 12:09:26 2017 -0400 +++ b/macros.xml Tue Jun 20 12:57:03 2017 -0400 |
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| @@ -6,24 +6,48 @@ <requirement type="package" version="@VERSION@">bioconductor-iwtomics</requirement> </requirements> </xml> + + <xml name="alignment-s"> + <conditional name="conditionalscale"> + <param name="alignment" type="select" label="Region alignment" help=""> + <option value="center">Center - Alignment on the central position</option> + <option value="left">Left - Alignment on the starting position</option> + <option value="right">Right - Alignment on the ending position</option> + <option value="scale">Scale - Scaling all regions to the same length</option> + </param> + <when value="center"> + <!-- fill gaps --> + <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" /> + </when> + <when value="left"> + <!-- fill gaps --> + <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" /> + </when> + <when value="right"> + <!-- fill gaps --> + <param name="fillgaps" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Use smoothing to fill gaps (NA measurements)" help="" /> + </when> + <when value="scale"> + <param name="scalegrid" type="integer" value="0" min="0" label="Number of grid points" help="Number of equally-spaced grid points over which the smoothed curves are evaluated." /> + </when> + </conditional> + </xml> + + <xml name="alignment"> + <param name="alignment" type="select" label="Region alignment" help=""> + <option value="center">Center - Alignment on the central position</option> + <option value="left">Left - Alignment on the starting position</option> + <option value="right">Right - Alignment on the ending position</option> + </param> + </xml> + <xml name="citations"> <citations> - <citation type="bibtex"> - @ARTICLE{ - iwt-functional-data, - author = {Pini, Alessia and Vantini, Simone}, - title = {Interval-Wise Testing for functional data}, - journal = {Journal of Nonparametric Statistics}, - year = {2017}, - volume = {29}, - number = {2}, - pages = {407-424} - } - </citation> + <citation type="doi">10.1080/10485252.2017.1306627</citation> <citation type="bibtex"> @MANUAL{ iwtomics, - author = {Cremona, Marzia A and Pini, Alessia and Chiaromonte, Francesca and Vantini, Simone}, + author = {Cremona, M.A. and Pini, A. and Chiaromonte, F. and Vantini, S.}, title = {IWTomics: Interval-Wise Testing for Omics Data}, note = {R package version 1.0.0}, year = {2017} @@ -31,4 +55,52 @@ </citation> </citations> </xml> + + <xml name="plot-params"> + <!-- average --> + <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" /> + <!-- average --> + <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" /> + <!-- conditional plot type --> + <conditional name="conditionalplottype"> + <!-- plot type --> + <param name="plottype" type="select" label="Plot type"> + <option value="boxplot">Pointwise quantile curves (boxplot)</option> + <option value="curves">Curves (aligned)</option> + </param> + <!-- conditional choice: plottype=boxplot --> + <when value="boxplot"> + <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn."> + <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" /> + <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" /> + <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" /> + <repeat name="probabilities" title="Probabilities"> + <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" /> + </repeat> + </section> + </when> + </conditional> + </xml> + + <xml name="plot-sum"> + <section name="plotsum" title="Summary plot" expanded="True"> + <!-- conditional group by --> + <conditional name="conditionalgroupby"> + <!-- group by --> + <param name="groupby" type="select" label="Group by" help="How tests should be grouped."> + <option value="none">No plot</option> + <option value="test">Group by test</option> + <option value="feature">Group by feature</option> + </param> + <when value="test"> + <param name="testalphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" /> + <param name="testonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" /> + </when> + <when value="feature"> + <param name="featurealphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" /> + <param name="featureonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" /> + </when> + </conditional> + </section> + </xml> </macros> \ No newline at end of file |
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| diff -r 0a17de046de0 -r 7dcc25a1a062 plotwithscale.xml --- a/plotwithscale.xml Mon Jun 19 12:09:26 2017 -0400 +++ b/plotwithscale.xml Tue Jun 20 12:57:03 2017 -0400 |
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| @@ -3,7 +3,7 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> + <!--<expand macro="requirements" />--> <command detect_errors="exit_code"> <![CDATA[ @@ -40,13 +40,7 @@ summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}' only_significant='${plotsum.conditionalgroupby.featureonlysig}' #end if - - >& /dev/null ]]> - <!-- - to print the stack add the following line at the end of the command and enable the corresponding entry in output - 2> "${stackerr}" - --> </command> <inputs> @@ -70,55 +64,14 @@ <section name="plotres" title="Plot IWTomics test results" expanded="True"> <!-- alpha --> <param name="alpha" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" /> - <!-- average --> - <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" /> - <!-- average --> - <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" /> - <!-- conditional plot type --> - <conditional name="conditionalplottype"> - <!-- plot type --> - <param name="plottype" type="select" label="Plot type"> - <option value="boxplot">Pointwise quantile curves (boxplot)</option> - <option value="curves">Curves (aligned)</option> - </param> - <!-- conditional choice: plottype=boxplot --> - <when value="boxplot"> - <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn."> - <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" /> - <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" /> - <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" /> - <repeat name="probabilities" title="Probabilities"> - <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" /> - </repeat> - </section> - </when> - </conditional> + <expand macro="plot-params" /> </section> <!-- summary plot --> - <section name="plotsum" title="Summary plot" expanded="True"> - <!-- conditional group by --> - <conditional name="conditionalgroupby"> - <!-- group by --> - <param name="groupby" type="select" label="Group by" help="How tests should be grouped."> - <option value="none">No plot</option> - <option value="test">Group by test</option> - <option value="feature">Group by feature</option> - </param> - <when value="test"> - <param name="testalphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" /> - <param name="testonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" /> - </when> - <when value="feature"> - <param name="featurealphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" /> - <param name="featureonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" /> - </when> - </conditional> - </section> + <expand macro="plot-sum" /> </inputs> <outputs> - <!--<data format="txt" name="stackerr" label="iwtomics.testandplot.stackerr.txt" from_work_dir="iwtomics.plotwithscale.stackerr.txt" />--> <data format="txt" name="adjustedpvalue" label="${tool.name} on ${on_string}: Adjusted p-value" from_work_dir="iwtomics.plotwithscale.adjustedpvalue.txt" /> <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.plotwithscale.iwtomicstestresults.pdf" /> <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.plotwithscale.summaryplot.pdf" /> |
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| diff -r 0a17de046de0 -r 7dcc25a1a062 testandplot.xml --- a/testandplot.xml Mon Jun 19 12:09:26 2017 -0400 +++ b/testandplot.xml Tue Jun 20 12:57:03 2017 -0400 |
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| @@ -3,7 +3,7 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> + <!--<expand macro="requirements" />--> <command detect_errors="exit_code"> <![CDATA[ @@ -48,13 +48,7 @@ summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}' only_significant='${plotsum.conditionalgroupby.featureonlysig}' #end if - - >& /dev/null ]]> - <!-- - to print the stack add the following line at the end of the command and enable the corresponding entry in output - 2> "${stackerr}" - --> </command> <inputs> @@ -102,55 +96,14 @@ <section name="plotres" title="Plot IWTomics test results" expanded="True"> <!-- alpha --> <param name="alpha" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" /> - <!-- average --> - <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" /> - <!-- average --> - <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" /> - <!-- conditional plot type --> - <conditional name="conditionalplottype"> - <!-- plot type --> - <param name="plottype" type="select" label="Plot type"> - <option value="boxplot">Pointwise quantile curves (boxplot)</option> - <option value="curves">Curves (aligned)</option> - </param> - <!-- conditional choice: plottype=boxplot --> - <when value="boxplot"> - <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn."> - <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" /> - <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" /> - <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" /> - <repeat name="probabilities" title="Probabilities"> - <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" /> - </repeat> - </section> - </when> - </conditional> + <expand macro="plot-params" /> </section> <!-- summary plot --> - <section name="plotsum" title="Summary plot" expanded="True"> - <!-- conditional group by --> - <conditional name="conditionalgroupby"> - <!-- group by --> - <param name="groupby" type="select" label="Group by" help="How tests should be grouped."> - <option value="none">No plot</option> - <option value="test">Group by test</option> - <option value="feature">Group by feature</option> - </param> - <when value="test"> - <param name="testalphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" /> - <param name="testonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" /> - </when> - <when value="feature"> - <param name="featurealphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" /> - <param name="featureonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" /> - </when> - </conditional> - </section> + <expand macro="plot-sum" /> </inputs> <outputs> - <!--<data format="txt" name="stackerr" label="iwtomics.testandplot.stackerr.txt" from_work_dir="iwtomics.testandplot.stackerr.txt" />--> <data format="txt" name="adjustedpvaluematrix" label="${tool.name} on ${on_string}: Adjusted p-value Matrix" from_work_dir="iwtomics.testandplot.adjustedpvalue.matrix.txt" /> <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.testandplot.iwtomicstestresults.pdf" /> <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.testandplot.summaryplot.pdf" /> |