Mercurial > repos > iuc > ggplot2_point

comparison ggplot_point.xml @ 12:156a2e14ce31 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
author iuc
date Fri, 09 Dec 2022 22:39:49 +0000
parents ba8be8bcbf8f
children 3e33010715f8
comparison
equal deleted inserted replaced
11:ba8be8bcbf8f 12:156a2e14ce31
1 <tool id="ggplot2_point" name="Scatterplot with ggplot2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> 1 <tool id="ggplot2_point" name="Scatterplot with ggplot2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <expand macro="bio_tools"/> 2 <expand macro="bio_tools"/>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <token name="@SIMPLE_GGLINE@">gg_line = geom_line(size=1, alpha=1, gg_factor)</token>
5 </macros> 6 </macros>
6 <expand macro="requirements"> 7 <expand macro="requirements">
7 <requirement type="package" version="2.0.0">r-svglite</requirement> 8 <requirement type="package" version="2.1.0">r-svglite</requirement>
8 </expand> 9 </expand>
9 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
10 cat '$script' && 11 cat '$script' &&
11 Rscript '$script' 12 Rscript '$script'
12 ]]></command> 13 ]]></command>
32 ## choosing whether to plot data as multiple groups on one plot(factoring) OR multiple groups on different plots 33 ## choosing whether to plot data as multiple groups on one plot(factoring) OR multiple groups on different plots
33 #if $adv.factor.factoring == "Multiple" 34 #if $adv.factor.factoring == "Multiple"
34 gg_facet = facet_wrap( ~ factor) 35 gg_facet = facet_wrap( ~ factor)
35 gg_factor = NULL 36 gg_factor = NULL
36 color_scale = NULL 37 color_scale = NULL
37 #if $adv.type_conditional.points.pointoptions == "default" 38 #if $adv.type_conditional.type_options == "lines":
39 @SIMPLE_GGLINE@
40 #elif $adv.type_conditional.points.pointoptions == "default"
38 gg_point = geom_point(size=1, alpha=1, gg_factor) 41 gg_point = geom_point(size=1, alpha=1, gg_factor)
39 gg_line = geom_line(size=1, alpha=1, gg_factor) 42 @SIMPLE_GGLINE@
40 #else 43 #else
41 gg_point = geom_point(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour='$adv.type_conditional.points.pointcolor', shape=as.numeric('$adv.type_conditional.points.shape')) 44 gg_point = geom_point(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour='$adv.type_conditional.points.pointcolor', shape=as.numeric('$adv.type_conditional.points.shape'))
42 gg_line = geom_line(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour='$adv.type_conditional.points.pointcolor', shape=as.numeric('$adv.type_conditional.points.shape')) 45 gg_line = geom_line(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour='$adv.type_conditional.points.pointcolor', shape=as.numeric('$adv.type_conditional.points.shape'))
43 #end if 46 #end if
44 47
46 49
47 #elif $adv.factor.factoring == "Single" 50 #elif $adv.factor.factoring == "Single"
48 gg_facet = NULL 51 gg_facet = NULL
49 gg_factor = aes(colour=factor(factor)) 52 gg_factor = aes(colour=factor(factor))
50 53
51 #if $adv.type_conditional.points.pointoptions == "default" 54 #if $adv.type_conditional.type_options == "lines":
55 @SIMPLE_GGLINE@
56 #elif $adv.type_conditional.points.pointoptions == "default"
52 gg_point = geom_point(size=1, alpha=1, gg_factor) 57 gg_point = geom_point(size=1, alpha=1, gg_factor)
53 gg_line = geom_line(size=1, alpha=1, gg_factor) 58 @SIMPLE_GGLINE@
54 #else 59 #else
55 gg_point = geom_point(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, gg_factor) 60 gg_point = geom_point(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, gg_factor, shape=as.numeric('$adv.type_conditional.points.shape')
56 gg_line = geom_line(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, gg_factor) 61 gg_line = geom_line(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, gg_factor, shape=as.numeric('$adv.type_conditional.points.shape')
57 #end if 62 #end if
58 63
59 #if $adv.factor.colororder == 1 64 #if $adv.factor.colororder == 1
60 color_scale = scale_colour_hue(direction='$adv.factor.colororder') 65 color_scale = scale_colour_hue(direction='$adv.factor.colororder')
61 #else 66 #else
66 #else 71 #else
67 gg_facet = NULL 72 gg_facet = NULL
68 gg_factor = NULL 73 gg_factor = NULL
69 color_scale = NULL 74 color_scale = NULL
70 75
71 #if $adv.type_conditional.points.pointoptions == "default" 76 #if $adv.type_conditional.type_options == "lines":
77 @SIMPLE_GGLINE@
78 #elif $adv.type_conditional.points.pointoptions == "default"
72 gg_point = geom_point(size=1, alpha=1, gg_factor) 79 gg_point = geom_point(size=1, alpha=1, gg_factor)
73 gg_line = geom_line(size=1, alpha=1, gg_factor) 80 @SIMPLE_GGLINE@
74 #else 81 #else
75 gg_point = geom_point(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour='$adv.type_conditional.points.pointcolor', shape=as.numeric('$adv.type_conditional.points.shape')) 82 gg_point = geom_point(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour='$adv.type_conditional.points.pointcolor', shape=as.numeric('$adv.type_conditional.points.shape'))
76 gg_line = geom_line(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour='$adv.type_conditional.points.pointcolor', shape=as.numeric('$adv.type_conditional.points.shape')) 83 gg_line = geom_line(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour='$adv.type_conditional.points.pointcolor', shape=as.numeric('$adv.type_conditional.points.shape'))
77 #end if 84 #end if
78 #end if 85 #end if
218 </conditional> 225 </conditional>
219 </section> 226 </section>
220 <param name="additional_output_format" value="pdf" /> 227 <param name="additional_output_format" value="pdf" />
221 <output name="output2" file="ggplot_point_result2.pdf" compare="sim_size" /> 228 <output name="output2" file="ggplot_point_result2.pdf" compare="sim_size" />
222 </test> 229 </test>
230 <!-- Test lines option -->
231 <test>
232 <param name="input1" value="mtcars.txt" ftype="tabular" />
233 <section name="adv">
234 <conditional name="type_conditional">
235 <param name="type_options" value="lines"/>
236 </conditional>
237 </section>
238 <param name="additional_output_format" value="pdf" />
239 <output name="output2" file="ggplot_line_result1.pdf" compare="sim_size" />
240 </test>
223 <!-- Test defined point options options--> 241 <!-- Test defined point options options-->
224 <test> 242 <test>
225 <param name="input1" value="mtcars.txt" ftype="tabular" /> 243 <param name="input1" value="mtcars.txt" ftype="tabular" />
226 <section name="adv"> 244 <section name="adv">
227 <conditional name="type_conditional"> 245 <conditional name="type_conditional">