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comparison plotwithscale.xml @ 76:7dcc25a1a062 draft

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Uploaded 20170620
author fabio
date Tue, 20 Jun 2017 12:57:03 -0400
parents 2bb6b44093ba
children 5893ad34d0ac
comparison
equal deleted inserted replaced
75:0a17de046de0 76:7dcc25a1a062
1 <tool id="iwtomics_plotwithscale" name="IWTomics Plot with Threshold" version="@VERSION@.0"> 1 <tool id="iwtomics_plotwithscale" name="IWTomics Plot with Threshold" version="@VERSION@.0">
2 <description>on Test Scale</description> 2 <description>on Test Scale</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <!--<expand macro="requirements" />-->
7 7
8 <command detect_errors="exit_code"> 8 <command detect_errors="exit_code">
9 <![CDATA[ 9 <![CDATA[
10 Rscript '$__tool_directory__/plotwithscale.R' adjustedpvalue='${adjustedpvalue}' iwtomicsrespdf='${iwtomicsrespdf}' iwtomicssumpdf='${iwtomicssumpdf}' 10 Rscript '$__tool_directory__/plotwithscale.R' adjustedpvalue='${adjustedpvalue}' iwtomicsrespdf='${iwtomicsrespdf}' iwtomicssumpdf='${iwtomicssumpdf}'
11 iwtomicsrdata='${rdata}' 11 iwtomicsrdata='${rdata}'
38 only_significant='${plotsum.conditionalgroupby.testonlysig}' 38 only_significant='${plotsum.conditionalgroupby.testonlysig}'
39 #elif $plotsum.conditionalgroupby.groupby == "feature": 39 #elif $plotsum.conditionalgroupby.groupby == "feature":
40 summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}' 40 summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}'
41 only_significant='${plotsum.conditionalgroupby.featureonlysig}' 41 only_significant='${plotsum.conditionalgroupby.featureonlysig}'
42 #end if 42 #end if
43
44 >& /dev/null
45 ]]> 43 ]]>
46 <!--
47 to print the stack add the following line at the end of the command and enable the corresponding entry in output
48 2> "${stackerr}"
49 -->
50 </command> 44 </command>
51 45
52 <inputs> 46 <inputs>
53 <!-- RData --> 47 <!-- RData -->
54 <param format="rdata" name="rdata" type="data" label="Select IWTomicsData object with test results" help="File created by 'IWTomics Test and Plot'." /> 48 <param format="rdata" name="rdata" type="data" label="Select IWTomicsData object with test results" help="File created by 'IWTomics Test and Plot'." />
68 62
69 <!-- plot IWTomics results --> 63 <!-- plot IWTomics results -->
70 <section name="plotres" title="Plot IWTomics test results" expanded="True"> 64 <section name="plotres" title="Plot IWTomics test results" expanded="True">
71 <!-- alpha --> 65 <!-- alpha -->
72 <param name="alpha" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" /> 66 <param name="alpha" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
73 <!-- average --> 67 <expand macro="plot-params" />
74 <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" />
75 <!-- average -->
76 <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" />
77 <!-- conditional plot type -->
78 <conditional name="conditionalplottype">
79 <!-- plot type -->
80 <param name="plottype" type="select" label="Plot type">
81 <option value="boxplot">Pointwise quantile curves (boxplot)</option>
82 <option value="curves">Curves (aligned)</option>
83 </param>
84 <!-- conditional choice: plottype=boxplot -->
85 <when value="boxplot">
86 <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
87 <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
88 <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
89 <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
90 <repeat name="probabilities" title="Probabilities">
91 <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
92 </repeat>
93 </section>
94 </when>
95 </conditional>
96 </section> 68 </section>
97 69
98 <!-- summary plot --> 70 <!-- summary plot -->
99 <section name="plotsum" title="Summary plot" expanded="True"> 71 <expand macro="plot-sum" />
100 <!-- conditional group by -->
101 <conditional name="conditionalgroupby">
102 <!-- group by -->
103 <param name="groupby" type="select" label="Group by" help="How tests should be grouped.">
104 <option value="none">No plot</option>
105 <option value="test">Group by test</option>
106 <option value="feature">Group by feature</option>
107 </param>
108 <when value="test">
109 <param name="testalphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
110 <param name="testonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
111 </when>
112 <when value="feature">
113 <param name="featurealphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
114 <param name="featureonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
115 </when>
116 </conditional>
117 </section>
118 </inputs> 72 </inputs>
119 73
120 <outputs> 74 <outputs>
121 <!--<data format="txt" name="stackerr" label="iwtomics.testandplot.stackerr.txt" from_work_dir="iwtomics.plotwithscale.stackerr.txt" />-->
122 <data format="txt" name="adjustedpvalue" label="${tool.name} on ${on_string}: Adjusted p-value" from_work_dir="iwtomics.plotwithscale.adjustedpvalue.txt" /> 75 <data format="txt" name="adjustedpvalue" label="${tool.name} on ${on_string}: Adjusted p-value" from_work_dir="iwtomics.plotwithscale.adjustedpvalue.txt" />
123 <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.plotwithscale.iwtomicstestresults.pdf" /> 76 <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.plotwithscale.iwtomicstestresults.pdf" />
124 <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.plotwithscale.summaryplot.pdf" /> 77 <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.plotwithscale.summaryplot.pdf" />
125 </outputs> 78 </outputs>
126 79