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comparison plot.xml @ 0:f370d221c284 draft default tip

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"planemo upload for repository https://github.com/shenwei356/csvtk commit 3a97e1b79bf0c6cdd37d5c8fb497b85531a563ab"
author nml
date Tue, 19 May 2020 17:10:23 -0400
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-1:000000000000 0:f370d221c284
1 <tool id="csvtk_plot" name="csvtk-plot" version="@VERSION@+@GALAXY_VERSION@">
2 <description> histogram, line/scatter plot, or boxplot based on column</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version_cmd" />
8 <command detect_errors="exit_code"><![CDATA[
9
10 ###################
11 ## Start Command ##
12 ###################
13 csvtk plot
14
15 #if $plot_type.plot == "histogram"
16 hist
17 #elif $plot_type.plot == "boxplot"
18 box
19 #elif $plot_type.plot == "line"
20 line
21 #end if
22
23 --num-cpus "\${GALAXY_SLOTS:-1}"
24
25 ## Add additional flags as specified ##
26 #######################################
27 $global_param.illegal_rows
28 $global_param.empty_rows
29 $global_param.header
30 $global_param.lazy_quotes
31
32 ## Set Tabular input/output flag if first input is tabular ##
33 #############################################################
34 #if $in_1.is_of_type("tabular"):
35 -t -T
36 #end if
37
38 ## Set input files ##
39 #####################
40 $in_1
41
42 ## Specific Plot Parameters ##
43 ##############################
44 #if $plot_type.plot == "histogram"
45 -f '$plot_type.column_text.in_text'
46 --color-index $plot_type.colour
47
48 #elif $plot_type.plot == "boxplot"
49 -f '$plot_type.column_text.in_text'
50 $plot_type.horizontal
51
52 #if $plot_type.group_field.select_group != "none"
53 -g '$plot_type.group_field.in_text'
54 #end if
55
56 #if $plot_type.box_width
57 --box-width '$plot_type.box_width'
58 #end if
59
60 #elif $plot_type.plot == "line"
61 $plot_type.scatter
62 -x '$plot_type.column_text.in_text_x'
63 -y '$plot_type.column_text.in_text_y'
64
65 #if $plot_type.group_field.select_group != "none"
66 -g '$plot_type.group_field.in_text'
67 #end if
68
69 $plot_type.label_location
70
71 #end if
72
73 ## General Plot Parameters ##
74 #############################
75
76 #if $plot_parameters.figure_height
77 --height '$plot_parameters.figure_height'
78 #end if
79
80 #if $plot_parameters.figure_width
81 --width '$plot_parameters.figure_width'
82 #end if
83
84 #if $plot_parameters.tick_width
85 --tick-width '$plot_parameters.tick_width'
86 #end if
87
88 #if $plot_parameters.title
89 --title '$plot_parameters.title'
90 #end if
91
92 #if $plot_parameters.x_label
93 --xlab '$plot_parameters.x_label'
94 #end if
95
96 #if $plot_parameters.min_x
97 --x-min '$plot_parameters.min_x'
98 #end if
99
100 #if $plot_parameters.max_x
101 --x-max '$plot_parameters.max_x'
102 #end if
103
104 #if $plot_parameters.y_label
105 --ylab '$plot_parameters.y_label'
106 #end if
107
108 #if $plot_parameters.min_y
109 --y-min '$plot_parameters.min_y'
110 #end if
111
112 #if $plot_parameters.max_y
113 --y-max '$plot_parameters.max_y'
114 #end if
115
116 ## To output ##
117 ###############
118 > plot.png
119
120 ]]></command>
121 <inputs>
122 <expand macro="singular_input"/>
123 <conditional name="plot_type">
124 <param name="plot" type="select" label="Select plot type">
125 <option value="histogram">Histogram</option>
126 <option value="boxplot">Boxplot</option>
127 <option value="line">Line/Scatter</option>
128 </param>
129 <when value="histogram">
130 <expand macro="plot_field" />
131 <param name="colour" type="integer"
132 min="1" max="7"
133 value="1"
134 argument="--color-index"
135 label="Select colour scheme"
136 help="Choose a number from 1-7"
137 />
138 </when>
139 <when value="boxplot" >
140 <expand macro="plot_field" />
141 <expand macro="groups_input" />
142 <param type="boolean" name="horizontal" label="Horizontal Box Plot" argument="--horiz"
143 checked="false"
144 falsevalue=""
145 truevalue="--horiz"
146 />
147 <param name="box_width" type="float"
148 label="Box Width (Optional)"
149 argument="--box-width"
150 optional="true"
151 />
152 </when>
153 <when value="line">
154 <param name="scatter" type="boolean" label="Scatter Plot" argument="--scatter"
155 checked="false"
156 falsevalue=""
157 truevalue="--scatter"
158 help="Plot only points, no lines"
159 />
160 <conditional name="column_text" >
161 <param type="select" name="select" label="Select input data columns for the X and Y axis based on:" >
162 <option value="string">Column Name</option>
163 <option value="column">Column Number</option>
164 </param>
165 <when value="column">
166 <param type="data_column" name="in_text_x"
167 data_ref="in_1"
168 multiple="false"
169 label="X-axis data column"
170 />
171 <param type="data_column" name="in_text_y"
172 data_ref="in_1"
173 multiple="false"
174 label="Y-axis data column"
175 />
176 </when>
177 <when value="string">
178 <param type="text" name="in_text_x"
179 optional="false"
180 label="X-axis data column"
181 help="Can use column name or column number">
182 <expand macro="text_sanitizer" />
183 </param>
184 <param type="text" name="in_text_y"
185 optional="false"
186 label="Y-axis data column"
187 help="Can use column name or column number">
188 </param>
189 </when>
190 </conditional>
191 <expand macro="groups_input" />
192 <param name="label_location" type="select" label="Label Location"
193 help="Only displays legend if a groups column is set">
194 <option value="--legend-left">Left edge of plot</option>
195 <option value="--legend-top">Top edge of plot</option>
196 </param>
197 </when>
198 </conditional>
199 <expand macro="global_plot_parameters" />
200 <expand macro="global_parameters" />
201 </inputs>
202 <outputs>
203 <data format="png" from_work_dir="plot.png" name="out_plot" label="${in_1.name} ${plot_type.plot}" />
204 </outputs>
205 <tests>
206 <test>
207 <param name="in_1" value="plot.csv" />
208 <conditional name="plot_type">
209 <param name="plot" value="histogram" />
210 <conditional name="column_text">
211 <param name="select" value="string" />
212 <param name="in_text" value="2" />
213 </conditional>
214 <param name="colour" value="2" />
215 </conditional>
216 <output name="out_plot" value="plot.png" ftype="png" compare="sim_size" delta="20000" />
217 </test>
218 <test>
219 <param name="in_1" value="plot.csv" />
220 <conditional name="plot_type">
221 <param name="plot" value="boxplot" />
222 <conditional name="column_text">
223 <param name="select" value="column" />
224 <param name="in_text" value="2" />
225 </conditional>
226 <conditional name="group_field">
227 <param name="select_group" value="string" />
228 <param name="in_text" value="1" />
229 </conditional>
230 <param name="horizontal" value="true" />
231 <param name="box_width" value="50.5" />
232 </conditional>
233 <output name="out_plot" value="plot_box.png" compare="sim_size" delta="20000" />
234 </test>
235 <test>
236 <param name="in_1" value="plot.csv" />
237 <conditional name="plot_type">
238 <param name="plot" value="line" />
239 <param name="scatter" value="true" />
240 <conditional name="column_text">
241 <param name="select" value="column" />
242 <param name="in_text_x" value="2" />
243 <param name="in_text_y" value="3" />
244 </conditional>
245 <conditional name="group_field">
246 <param name="select_group" value="string" />
247 <param name="in_text" value="1" />
248 </conditional>
249 </conditional>
250 <output name="out_plot" value="plot_scatter.png" compare="sim_size" delta="20000" />
251 </test>
252 <test>
253 <param name="in_1" value="plot.csv" />
254 <conditional name="plot_type">
255 <param name="plot" value="line" />
256 <param name="scatter" value="false" />
257 <conditional name="column_text">
258 <param name="select" value="column" />
259 <param name="in_text_x" value="2" />
260 <param name="in_text_y" value="3" />
261 </conditional>
262 <conditional name="group_field">
263 <param name="select_group" value="string" />
264 <param name="in_text" value="1" />
265 </conditional>
266 <param name="label_location" value="--legend-top" />
267 </conditional>
268 <section name="plot_parameters">
269 <param name="figure_height" value="10.1" />
270 <param name="figure_width" value="6.6" />
271 <param name="tick_width" value="2.1" />
272 <param name="title" value="Test" />
273 <param name="x_label" value="Potentially Broken" />
274 <param name="min_x" value="1.1" />
275 <param name="max_x" value="109.1" />
276 <param name="y_label" value="How High Can We Go?" />
277 <param name="min_y" value="-10.4" />
278 <param name="max_y" value="141.9" />
279 </section>
280 <output name="out_plot" value="line_all_param.png" compare="sim_size" delta="20000" />
281 </test>
282 </tests>
283 <help><![CDATA[
284
285 Csvtk - Plot Help
286 -----------------
287
288 Info
289 ####
290
291 Use Csvtk-Plot to plot histograms, line plots / scatter plots, or boxplots.
292
293 Specify a column or a couple of columns from an input CSV/TSV dataset to generate wanted plots fast.
294
295 .. class:: warningmark
296
297 Single quotes are not allowed in text inputs!
298
299 @HELP_INPUT_DATA@
300
301
302 @HELP_END_STATEMENT@
303
304
305 ]]></help>
306 <expand macro="citations" />
307 </tool>