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comparison xy_plot.xml @ 7:afb09b6aee95 draft

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author saskia-hiltemann
date Fri, 30 Oct 2015 06:09:30 -0400
parents f259b7f33591
children c3cd8bf8f3b5
comparison
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6:8a6e2b2776d2 7:afb09b6aee95
1 <tool id="XY_Plot_1_multiformat" name="Plotting tool 2" version="1.0.1"> 1 <tool id="XY_Plot_1_multiformat" name="Plotting tool" version="1.0.1">
2 <description>for multiple series and graph types</description> 2 <description>for multiple series and graph types and multiple output types</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.1.2">R</requirement> 4 <requirement type="package" version="3.1.2">R</requirement>
5 <requirement type="package" version="2.11.1">fontconfig</requirement> 5 <requirement type="package" version="2.11.1">fontconfig</requirement>
6 </requirements> 6 </requirements>
7 <command interpreter="bash">r_wrapper.sh $script_file</command> 7 <command interpreter="bash">r_wrapper.sh $script_file</command>
8 8
9 <inputs> 9 <inputs>
10 <param name="main" type="text" value="" label="Plot Title"/> 10 <param name="main" type="text" value="" label="Plot Title"/>
11 <param name="xlab" type="text" value="" label="Label for x axis"/> 11 <param name="xlab" type="text" value="" label="Label for x axis"/>
12 <param name="ylab" type="text" value="" label="Label for y axis"/> 12 <param name="ylab" type="text" value="" label="Label for y axis"/>
13 <param name="ftype" type="select" label="File Type">
14 <option value="pdf">PDF</option>
15 <option value="png">PNG</option>
16 <option value="jpeg">JPEG</option>
17 <option value="bmp">BMP</option>
18 <option value="tiff">TIFF</option>
19 </param>
13 <repeat name="series" title="Series"> 20 <repeat name="series" title="Series">
14 <param name="input" type="data" format="tabular" label="Dataset"/> 21 <param name="input" type="data" format="tabular" label="Dataset"/>
15 <param name="xcol" type="data_column" data_ref="input" label="Column for x axis"/> 22 <param name="xcol" type="data_column" data_ref="input" label="Column for x axis"/>
16 <param name="ycol" type="data_column" data_ref="input" label="Column for y axis"/> 23 <param name="ycol" type="data_column" data_ref="input" label="Column for y axis"/>
17 <conditional name="series_type"> 24 <conditional name="series_type">
77 y${i} = s${i}[,${s.ycol}] 84 y${i} = s${i}[,${s.ycol}]
78 xrange = range( x${i}, xrange ) 85 xrange = range( x${i}, xrange )
79 yrange = range( y${i}, yrange ) 86 yrange = range( y${i}, yrange )
80 #end for 87 #end for
81 ## Open output PDF file 88 ## Open output PDF file
82 png( "${out_file1}" , type="cairo") 89 #if $ftype.value == "pdf"
90 pdf("outfile.pdf")
91 #else
92 "${ftype}"( "outfile.${ftype}" , type="cairo")
93 #end if
83 ## Dummy plot for axis / labels 94 ## Dummy plot for axis / labels
84 plot( NULL, type="n", xlim=xrange, ylim=yrange, main="${main}", xlab="${xlab}", ylab="${ylab}" ) 95 plot( NULL, type="n", xlim=xrange, ylim=yrange, main="${main}", xlab="${xlab}", ylab="${ylab}" )
85 ## Plot each series 96 ## Plot each series
86 #for $i, $s in enumerate( $series ) 97 #for $i, $s in enumerate( $series )
87 #if $s.series_type['type'] == "line" 98 #if $s.series_type['type'] == "line"
94 devname = dev.off() 105 devname = dev.off()
95 </configfile> 106 </configfile>
96 </configfiles> 107 </configfiles>
97 108
98 <outputs> 109 <outputs>
99 <data format="png" name="out_file1" /> 110 <data format="pdf" name="out_file1" from_work_dir="outfile.pdf" >
111 <filter>(ftype == 'pdf') </filter>
112 </data>
113 <data format="png" name="out_file2" from_work_dir="outfile.png">
114 <filter>(ftype == 'png') </filter>
115 </data>
116 <data format="jpg" name="out_file3" from_work_dir="outfile.jpeg">
117 <filter>(ftype == 'jpeg') </filter>
118 </data>
119 <data format="bmp" name="out_file4" from_work_dir="outfile.bmp">
120 <filter>(ftype == 'bmp') </filter>
121 </data>
122 <data format="tiff" name="out_file5" from_work_dir="outfile.tiff">
123 <filter>(ftype == 'tiff') </filter>
124 </data>
100 </outputs> 125 </outputs>
101 126
102 <tests> 127 <tests>
103 <test> 128 <test>
104 <param name="main" value="Example XY Plot"/> 129 <param name="main" value="Example XY Plot PDF"/>
105 <param name="xlab" value="Column 1"/> 130 <param name="xlab" value="Column 1"/>
106 <param name="ylab" value="Column 2"/> 131 <param name="ylab" value="Column 2"/>
107 <param name="input" value="2.tabular" ftype="tabular"/> 132 <param name="ftype" value="pdf"/>
108 <param name="xcol" value="1"/> 133 <param name="input" value="2.tabular" ftype="tabular"/>
109 <param name="ycol" value="2"/> 134 <param name="xcol" value="1"/>
110 <param name="type" value="line"/> 135 <param name="ycol" value="2"/>
111 <param name="lty" value="2"/> 136 <param name="type" value="line"/>
112 <param name="col" value="2"/> 137 <param name="lty" value="2"/>
113 <param name="lwd" value="1.0"/> 138 <param name="col" value="2"/>
114 <output name="out_file1" file="XY_Plot_1_out.pdf"/> 139 <param name="lwd" value="1.0"/>
140 <output name="out_file1" file="XY_Plot_1_multi_out.pdf" md5="83f82e036bdd7fcd51f29e3b7a05c19b"/>
141 </test>
142 <test>
143 <param name="main" value="Example XY Plot PNG"/>
144 <param name="xlab" value="Column 1"/>
145 <param name="ylab" value="Column 2"/>
146 <param name="ftype" value="png"/>
147 <param name="input" value="2.tabular" ftype="tabular"/>
148 <param name="xcol" value="1"/>
149 <param name="ycol" value="2"/>
150 <param name="type" value="line"/>
151 <param name="lty" value="2"/>
152 <param name="col" value="2"/>
153 <param name="lwd" value="1.0"/>
154 <output name="out_file2" file="XY_Plot_1_multi_out.png" md5="777f98fc9a29c3a02ce4da2fa61437c9"/>
155 </test>
156 <test>
157 <param name="main" value="Example XY Plot JPEG"/>
158 <param name="xlab" value="Column 1"/>
159 <param name="ylab" value="Column 2"/>
160 <param name="ftype" value="jpeg"/>
161 <param name="input" value="2.tabular" ftype="tabular"/>
162 <param name="xcol" value="1"/>
163 <param name="ycol" value="2"/>
164 <param name="type" value="line"/>
165 <param name="lty" value="2"/>
166 <param name="col" value="2"/>
167 <param name="lwd" value="1.0"/>
168 <output name="out_file3" file="XY_Plot_1_multi_out.jpeg" md5="609f009b8cd92c0662cb39d6e2eb8cc7"/>
169 </test>
170 <test>
171 <param name="main" value="Example XY Plot BMP"/>
172 <param name="xlab" value="Column 1"/>
173 <param name="ylab" value="Column 2"/>
174 <param name="ftype" value="bmp"/>
175 <param name="input" value="2.tabular" ftype="tabular"/>
176 <param name="xcol" value="1"/>
177 <param name="ycol" value="2"/>
178 <param name="type" value="line"/>
179 <param name="lty" value="2"/>
180 <param name="col" value="2"/>
181 <param name="lwd" value="1.0"/>
182 <output name="out_file4" file="XY_Plot_1_multi_out.bmp" md5="a036aa3d0bbc0ff58664077cb5c8e04a"/>
183 </test>
184 <test>
185 <param name="main" value="Example XY Plot TIFF"/>
186 <param name="xlab" value="Column 1"/>
187 <param name="ylab" value="Column 2"/>
188 <param name="ftype" value="tiff"/>
189 <param name="input" value="2.tabular" ftype="tabular"/>
190 <param name="xcol" value="1"/>
191 <param name="ycol" value="2"/>
192 <param name="type" value="line"/>
193 <param name="lty" value="2"/>
194 <param name="col" value="2"/>
195 <param name="lwd" value="1.0"/>
196 <output name="out_file5" file="XY_Plot_1_multi_out.tiff" md5="e6ba5639144b23480c556e2185bb5d9a"/>
115 </test> 197 </test>
116 </tests> 198 </tests>
117 <help> 199 <help>
118 .. class:: infomark 200 .. class:: infomark
119 201