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comparison testandplot.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_testandplot" name="IWTomics Test" version="@VERSION@.0"> 1 <tool id="iwtomics_testandplot" name="IWTomics Test" version="@VERSION@.0">
2 <description>and Plot</description> 2 <description>and Plot</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 '$__tool_directory__/testandplot.R' adjustedpvaluematrix='${adjustedpvaluematrix}' iwtomicsrespdf='${iwtomicsrespdf}' iwtomicssumpdf='${iwtomicssumpdf}' iwtomicsrdata='${iwtomicsrdata}' iwtomicstests='${iwtomicstests}' iwtomicsselectedfeatures='${iwtomicsselectedfeatures}' 10 Rscript '$__tool_directory__/testandplot.R' adjustedpvaluematrix='${adjustedpvaluematrix}' iwtomicsrespdf='${iwtomicsrespdf}' iwtomicssumpdf='${iwtomicssumpdf}' iwtomicsrdata='${iwtomicsrdata}' iwtomicstests='${iwtomicstests}' iwtomicsselectedfeatures='${iwtomicsselectedfeatures}'
11 regionids='${regionids}' 11 regionids='${regionids}'
46 only_significant='${plotsum.conditionalgroupby.testonlysig}' 46 only_significant='${plotsum.conditionalgroupby.testonlysig}'
47 #elif $plotsum.conditionalgroupby.groupby == "feature": 47 #elif $plotsum.conditionalgroupby.groupby == "feature":
48 summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}' 48 summaryalpha='${plotsum.conditionalgroupby.featurealphaplot}'
49 only_significant='${plotsum.conditionalgroupby.featureonlysig}' 49 only_significant='${plotsum.conditionalgroupby.featureonlysig}'
50 #end if 50 #end if
51
52 >& /dev/null
53 ]]> 51 ]]>
54 <!--
55 to print the stack add the following line at the end of the command and enable the corresponding entry in output
56 2> "${stackerr}"
57 -->
58 </command> 52 </command>
59 53
60 <inputs> 54 <inputs>
61 <!-- RData --> 55 <!-- RData -->
62 <param format="rdata" name="rdata" type="data" label="Select IWTomicsData object" help="File created by 'IWTomics Load Smooth and Plot'." /> 56 <param format="rdata" name="rdata" type="data" label="Select IWTomicsData object" help="File created by 'IWTomics Load Smooth and Plot'." />
100 94
101 <!-- plot IWTomics results --> 95 <!-- plot IWTomics results -->
102 <section name="plotres" title="Plot IWTomics test results" expanded="True"> 96 <section name="plotres" title="Plot IWTomics test results" expanded="True">
103 <!-- alpha --> 97 <!-- alpha -->
104 <param name="alpha" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" /> 98 <param name="alpha" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
105 <!-- average --> 99 <expand macro="plot-params" />
106 <param name="average" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot the mean curves" />
107 <!-- average -->
108 <param name="size" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Plot sample size in each position" />
109 <!-- conditional plot type -->
110 <conditional name="conditionalplottype">
111 <!-- plot type -->
112 <param name="plottype" type="select" label="Plot type">
113 <option value="boxplot">Pointwise quantile curves (boxplot)</option>
114 <option value="curves">Curves (aligned)</option>
115 </param>
116 <!-- conditional choice: plottype=boxplot -->
117 <when value="boxplot">
118 <section name="probabilitiessection" title="Probabilities" expanded="True" help="Probabilities corresponding to the quantile curves to be drawn.">
119 <param name="prob0" size="3" type="float" value="0.25" min="0.0" max="1.0" label="Probability" />
120 <param name="prob1" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
121 <param name="prob2" size="3" type="float" value="0.75" min="0.0" max="1.0" label="Probability" />
122 <repeat name="probabilities" title="Probabilities">
123 <param name="prob" size="3" type="float" value="0.5" min="0.0" max="1.0" label="Probability" />
124 </repeat>
125 </section>
126 </when>
127 </conditional>
128 </section> 100 </section>
129 101
130 <!-- summary plot --> 102 <!-- summary plot -->
131 <section name="plotsum" title="Summary plot" expanded="True"> 103 <expand macro="plot-sum" />
132 <!-- conditional group by -->
133 <conditional name="conditionalgroupby">
134 <!-- group by -->
135 <param name="groupby" type="select" label="Group by" help="How tests should be grouped.">
136 <option value="none">No plot</option>
137 <option value="test">Group by test</option>
138 <option value="feature">Group by feature</option>
139 </param>
140 <when value="test">
141 <param name="testalphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
142 <param name="testonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
143 </when>
144 <when value="feature">
145 <param name="featurealphaplot" size="3" type="float" value="0.05" min="0.0" max="1.0" label="Level of the test (alpha)" />
146 <param name="featureonlysig" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Plot only significant tests" />
147 </when>
148 </conditional>
149 </section>
150 </inputs> 104 </inputs>
151 105
152 <outputs> 106 <outputs>
153 <!--<data format="txt" name="stackerr" label="iwtomics.testandplot.stackerr.txt" from_work_dir="iwtomics.testandplot.stackerr.txt" />-->
154 <data format="txt" name="adjustedpvaluematrix" label="${tool.name} on ${on_string}: Adjusted p-value Matrix" from_work_dir="iwtomics.testandplot.adjustedpvalue.matrix.txt" /> 107 <data format="txt" name="adjustedpvaluematrix" label="${tool.name} on ${on_string}: Adjusted p-value Matrix" from_work_dir="iwtomics.testandplot.adjustedpvalue.matrix.txt" />
155 <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.testandplot.iwtomicstestresults.pdf" /> 108 <data format="pdf" name="iwtomicsrespdf" label="${tool.name} on ${on_string}: Plotted Test Results" from_work_dir="iwtomics.testandplot.iwtomicstestresults.pdf" />
156 <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.testandplot.summaryplot.pdf" /> 109 <data format="pdf" name="iwtomicssumpdf" label="${tool.name} on ${on_string}: Summary Plot" from_work_dir="iwtomics.testandplot.summaryplot.pdf" />
157 <data format="rdata" name="iwtomicsrdata" label="${tool.name} on ${on_string}: IWTomicsData Object with Test Results" from_work_dir="iwtomics.testandplot.RData" /> 110 <data format="rdata" name="iwtomicsrdata" label="${tool.name} on ${on_string}: IWTomicsData Object with Test Results" from_work_dir="iwtomics.testandplot.RData" />
158 <data format="tabular" name="iwtomicstests" label="${tool.name} on ${on_string}: Test IDs" from_work_dir="iwtomics.testandplot.tests.txt" /> 111 <data format="tabular" name="iwtomicstests" label="${tool.name} on ${on_string}: Test IDs" from_work_dir="iwtomics.testandplot.tests.txt" />