Mercurial > repos > iuc > ggplot2_point
comparison ggplot_point.xml @ 11:d0fc8b746d57 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 075aa3ab0ebc5eef83aac753a2cac7dffe2c6b0c
| author | iuc |
|---|---|
| date | Fri, 02 Dec 2022 09:35:49 +0000 |
| parents | 299307abd804 |
| children | 5fe1dc76176e |
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| 10:299307abd804 | 11:d0fc8b746d57 |
|---|---|
| 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="2.0.0">r-svglite</requirement> |
| 8 </expand> | 9 </expand> |
| 9 <command detect_errors="exit_code"><![CDATA[ | 10 <command detect_errors="exit_code"><![CDATA[ |
| 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=$adv.type_conditional.points.alpha, gg_factor) |
| 56 gg_line = geom_line(size=$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) |
| 57 #end if | 62 #end if |
| 58 | 63 |
| 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"> |