Mercurial > repos > iuc > ggplot2_point
annotate ggplot_point.xml @ 14:5298e06f14f9 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6737c924917eea8c009c30d7f9917d5a341b9948
author | iuc |
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date | Mon, 30 Sep 2024 15:40:11 +0000 |
parents | 3b12bf9b4b87 |
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rev | line source |
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13
3b12bf9b4b87
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit d7460b880c9b329465b1616d1e6ab33d45f3893c
iuc
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1 <tool id="ggplot2_point" name="Scatterplot with ggplot2" version="@TOOL_VERSION@+galaxy1" profile="20.01"> |
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1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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2 <macros> |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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3 <import>macros.xml</import> |
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d0fc8b746d57
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 075aa3ab0ebc5eef83aac753a2cac7dffe2c6b0c
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4 <token name="@SIMPLE_GGLINE@">gg_line = geom_line(size=1, alpha=1, gg_factor)</token> |
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1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
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5 </macros> |
14
5298e06f14f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6737c924917eea8c009c30d7f9917d5a341b9948
iuc
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6 <expand macro="bio_tools"/> |
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9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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7 <expand macro="requirements"> |
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5fe1dc76176e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 843a94f53c808d098def353b0bc5f7f554d9e1af
iuc
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8 <requirement type="package" version="2.1.0">r-svglite</requirement> |
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9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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9 </expand> |
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1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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10 <command detect_errors="exit_code"><![CDATA[ |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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11 cat '$script' && |
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9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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12 Rscript '$script' |
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1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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13 ]]></command> |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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14 <configfiles> |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
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15 <configfile name="script"><![CDATA[ |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
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16 @R_INIT@ |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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17 |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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18 ## Import library |
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9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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19 library(ggplot2) |
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1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
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20 |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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21 @XY_SCALING@ |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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22 |
2
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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23 @THEME@ |
0
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
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24 |
2
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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25 @LEGEND@ |
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1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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26 |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
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27 input <- read.csv('$input1', sep='\t', header=TRUE) |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
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28 |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
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29 ## renaming columns so ggplot can use them |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
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30 names(input)[$xplot] <- "xcol" |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
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31 names(input)[$yplot] <- "ycol" |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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32 |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
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33 ## choosing whether to plot data as multiple groups on one plot(factoring) OR multiple groups on different plots |
2
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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34 #if $adv.factor.factoring == "Multiple" |
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1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
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35 gg_facet = facet_wrap( ~ factor) |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
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36 gg_factor = NULL |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
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37 color_scale = NULL |
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d0fc8b746d57
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 075aa3ab0ebc5eef83aac753a2cac7dffe2c6b0c
iuc
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38 #if $adv.type_conditional.type_options == "lines": |
d0fc8b746d57
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 075aa3ab0ebc5eef83aac753a2cac7dffe2c6b0c
iuc
parents:
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39 @SIMPLE_GGLINE@ |
d0fc8b746d57
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 075aa3ab0ebc5eef83aac753a2cac7dffe2c6b0c
iuc
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40 #elif $adv.type_conditional.points.pointoptions == "default" |
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1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
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41 gg_point = geom_point(size=1, alpha=1, gg_factor) |
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d0fc8b746d57
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 075aa3ab0ebc5eef83aac753a2cac7dffe2c6b0c
iuc
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42 @SIMPLE_GGLINE@ |
0
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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43 #else |
10
299307abd804
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
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44 gg_point = geom_point(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour='$adv.type_conditional.points.pointcolor', shape=as.numeric('$adv.type_conditional.points.shape')) |
299307abd804
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
iuc
parents:
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45 gg_line = geom_line(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour='$adv.type_conditional.points.pointcolor', shape=as.numeric('$adv.type_conditional.points.shape')) |
0
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
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46 #end if |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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47 |
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9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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48 names(input)[$adv.factor.factorcol] <- "factor" |
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1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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49 |
2
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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50 #elif $adv.factor.factoring == "Single" |
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1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
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51 gg_facet = NULL |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
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52 gg_factor = aes(colour=factor(factor)) |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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53 |
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d0fc8b746d57
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 075aa3ab0ebc5eef83aac753a2cac7dffe2c6b0c
iuc
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54 #if $adv.type_conditional.type_options == "lines": |
d0fc8b746d57
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 075aa3ab0ebc5eef83aac753a2cac7dffe2c6b0c
iuc
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55 @SIMPLE_GGLINE@ |
d0fc8b746d57
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 075aa3ab0ebc5eef83aac753a2cac7dffe2c6b0c
iuc
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56 #elif $adv.type_conditional.points.pointoptions == "default" |
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9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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57 gg_point = geom_point(size=1, alpha=1, gg_factor) |
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d0fc8b746d57
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 075aa3ab0ebc5eef83aac753a2cac7dffe2c6b0c
iuc
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58 @SIMPLE_GGLINE@ |
2
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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59 #else |
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3b12bf9b4b87
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit d7460b880c9b329465b1616d1e6ab33d45f3893c
iuc
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60 gg_point = geom_point(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, gg_factor, shape=as.numeric('$adv.type_conditional.points.shape')) |
3b12bf9b4b87
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit d7460b880c9b329465b1616d1e6ab33d45f3893c
iuc
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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')) |
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9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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62 #end if |
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1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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63 |
4
52b8083a6159
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit d1da3cf72a15d88fc265edc5d64e6b820b6a2b2f
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64 #if $adv.factor.colororder == 1 |
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9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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65 color_scale = scale_colour_hue(direction='$adv.factor.colororder') |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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66 #else |
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52b8083a6159
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit d1da3cf72a15d88fc265edc5d64e6b820b6a2b2f
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67 color_scale = scale_color_brewer(palette='$adv.factor.colors', direction='$adv.factor.colororder') |
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9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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68 #end if |
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1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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69 |
2
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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70 names(input)[$adv.factor.factorcol] <- "factor" |
0
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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71 #else |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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72 gg_facet = NULL |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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73 gg_factor = NULL |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
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74 color_scale = NULL |
0
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
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75 |
11
d0fc8b746d57
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 075aa3ab0ebc5eef83aac753a2cac7dffe2c6b0c
iuc
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76 #if $adv.type_conditional.type_options == "lines": |
d0fc8b746d57
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 075aa3ab0ebc5eef83aac753a2cac7dffe2c6b0c
iuc
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77 @SIMPLE_GGLINE@ |
d0fc8b746d57
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 075aa3ab0ebc5eef83aac753a2cac7dffe2c6b0c
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78 #elif $adv.type_conditional.points.pointoptions == "default" |
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79 gg_point = geom_point(size=1, alpha=1, gg_factor) |
11
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 075aa3ab0ebc5eef83aac753a2cac7dffe2c6b0c
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80 @SIMPLE_GGLINE@ |
2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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81 #else |
10
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
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82 gg_point = geom_point(size=$adv.type_conditional.points.size, alpha=$adv.type_conditional.points.alpha, colour='$adv.type_conditional.points.pointcolor', shape=as.numeric('$adv.type_conditional.points.shape')) |
299307abd804
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 847c77a54204433d210cd8a1234474d014628424
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83 gg_line = geom_line(size=$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')) |
2
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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84 #end if |
0
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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85 #end if |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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86 |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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87 @TRANSFORM@ |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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88 |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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89 ##axis label custization |
2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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90 #if $adv.axis_title_customization.axis_customization == "default" |
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1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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91 gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL)) |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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92 #else |
9
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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93 gg_axistitle = theme(axis.title = element_text(color = '$adv.axis_text_customization.color', size = $adv.axis_text_customization.size, face = '$adv.axis_text_customization.face')) |
0
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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94 #end if |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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95 |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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96 ##axis text(tick) custization |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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97 #if $adv.axis_text_customization.axis_customization == "default" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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98 gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL)) |
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99 #else |
9
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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100 gg_axistext = theme(axis.text = element_text(color = '$adv.axis_text_customization.color', size = $adv.axis_text_customization.size, face = '$adv.axis_text_customization.face')) |
0
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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101 #end if |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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102 |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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103 ##plot title custimization |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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104 #if $adv.plot_title_customization.axis_customization == "default" |
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1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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105 gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL)) |
1bff6682e780
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106 #else |
9
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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107 gg_plottitle = theme(plot.title = element_text(color='$adv.axis_text_customization.color', size=$adv.axis_text_customization.size, face='$adv.axis_text_customization.face')) |
0
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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108 #end if |
1bff6682e780
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109 |
1bff6682e780
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110 ## grid line customization |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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111 #if $adv.gridlinecust == "default" |
0
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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112 gg_gridline = NULL |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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113 #elif $adv.gridlinecust == "hidemajor" |
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1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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114 gg_gridline = theme(panel.grid.major = element_blank()) |
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115 #elif $adv.gridlinecust == "hideminor" |
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1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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116 gg_gridline = theme(panel.grid.minor = element_blank()) |
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117 #elif $adv.gridlinecust == "hideboth" |
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1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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118 gg_gridline = theme(panel.grid.minor = element_blank(), panel.grid.major = element_blank()) |
1bff6682e780
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119 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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120 |
4
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit d1da3cf72a15d88fc265edc5d64e6b820b6a2b2f
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121 ## choose between graph types (points/lines/both) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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122 #if $adv.type_conditional.type_options == "points" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit d1da3cf72a15d88fc265edc5d64e6b820b6a2b2f
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123 gg_line = NULL |
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1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
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124 #elif $adv.type_conditional.type_options == "lines" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit d1da3cf72a15d88fc265edc5d64e6b820b6a2b2f
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125 gg_point = NULL |
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126 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit d1da3cf72a15d88fc265edc5d64e6b820b6a2b2f
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127 |
0
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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128 #this is the actual ggplot command to make the final plot(s) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit d1da3cf72a15d88fc265edc5d64e6b820b6a2b2f
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129 plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet + |
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130 gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('$title') + xlab('$xlab') + ylab('$ylab')+ |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
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131 gg_axistitle + gg_axistext + gg_plottitle + gg_gridline |
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132 |
2
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133 @SAVE_OUTPUT@ |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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134 ]]></configfile> |
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135 </configfiles> |
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136 <inputs> |
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137 <param name="input1" type="data" format="tabular" label="Input in tabular format" /> |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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138 <param name="xplot" type="integer" value="8" label="Column to plot on x-axis" /> |
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139 <param name="yplot" type="integer" value="9" label="Column to plot on y-axis" /> |
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140 |
1bff6682e780
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141 <expand macro="title" /> |
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142 <expand macro="xy_lab" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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143 <section name="adv" title="Advanced options"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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144 <conditional name="type_conditional"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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145 <param name="type_options" type="select" label="Type of plot" > |
1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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146 <option value="points">Points only (default)</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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147 <option value="lines">Lines only </option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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148 <option value="pointslines">Points and Lines</option> |
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1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
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149 </param> |
9
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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150 <when value ="points"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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151 <expand macro="points_options"/> |
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152 </when> |
9
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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153 <when value="pointslines"> |
1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents:
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154 <expand macro="points_options"/> |
2
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
diff
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|
155 </when> |
9
1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents:
8
diff
changeset
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156 <when value="lines"/> |
2
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
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changeset
|
157 </conditional> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
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changeset
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158 <conditional name="factor"> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
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changeset
|
159 <param name="factoring" type="select" label="Plotting multiple groups" > |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
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changeset
|
160 <option value="Default" selected="true">No thanks - just plot the data as one group</option> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
diff
changeset
|
161 <option value="Single">Plot multiple groups of data on one plot</option> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
diff
changeset
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162 <option value="Multiple">Plot multiple groups of data on individual plots</option> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
diff
changeset
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163 </param> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
diff
changeset
|
164 <when value="Default"> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
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changeset
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165 <!--Do nothing here --> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
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changeset
|
166 </when> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
diff
changeset
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167 <when value="Single"> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
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168 <param name="factorcol" type="integer" value="1" label="column differentiating the different groups" /> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
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169 <expand macro="colors" /> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
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170 <param name="colororder" type="select" label="Reverse color scheme" > |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
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171 <option value="1">Default order of color scheme</option> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
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changeset
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172 <option value="-1">Reverse the order of my color scheme</option> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
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173 </param> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
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changeset
|
174 </when> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
diff
changeset
|
175 <when value="Multiple"> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
diff
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|
176 <param name="factorcol" type="integer" value="1" label="column differentiating the different groups" /> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
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177 </when> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
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178 </conditional> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
diff
changeset
|
179 <conditional name="axis_title_customization"> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
diff
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|
180 <expand macro="axis_customization" label="Axis title options" /> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
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changeset
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181 </conditional> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
diff
changeset
|
182 <conditional name="axis_text_customization"> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
diff
changeset
|
183 <expand macro="axis_customization" label="Axis text options" /> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
diff
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184 </conditional> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
diff
changeset
|
185 <conditional name="plot_title_customization"> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
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changeset
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186 <expand macro="axis_customization" label="Plot title options" /> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
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187 </conditional> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
diff
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188 <param name="gridlinecust" type="select" label="Grid lines"> |
9
1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents:
8
diff
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189 <option value="default">Default grid lines</option> |
1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents:
8
diff
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190 <option value="hidemajor">Hide major grid lines</option> |
1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents:
8
diff
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191 <option value="hideminor">Hide minor grid lines</option> |
1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents:
8
diff
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192 <option value="hideboth">Hide major and minor grid lines</option> |
0
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff
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193 </param> |
2
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
diff
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194 <expand macro="transform" /> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
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diff
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195 <expand macro="xy_scaling" /> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
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diff
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196 <expand macro="theme" /> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
diff
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197 <expand macro="legend" /> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
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198 </section> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
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199 <section name="out" title="Output Options" expanded="true"> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
diff
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200 <expand macro="dimensions" /> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
diff
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|
201 </section> |
0
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff
changeset
|
202 </inputs> |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff
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|
203 <outputs> |
2
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
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204 <expand macro="additional_output" /> |
0
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff
changeset
|
205 </outputs> |
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff
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|
206 <tests> |
14
5298e06f14f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6737c924917eea8c009c30d7f9917d5a341b9948
iuc
parents:
13
diff
changeset
|
207 <test expect_num_outputs="2"> |
0
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff
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|
208 <param name="input1" value="mtcars.txt" ftype="tabular" /> |
2
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
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209 <param name="additional_output_format" value="pdf" /> |
9a482995958c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit f9fb73a88ab8b52ce11c25a966d4fe99e67c9fbf
iuc
parents:
0
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210 <output name="output2" file="ggplot_point_result1.pdf" compare="sim_size" /> |
0
1bff6682e780
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6e466ce83e2e5c0dd0ba30356d0488cf74574b8f
iuc
parents:
diff
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211 </test> |
9
1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents:
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212 <!-- Test text options--> |
14
5298e06f14f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6737c924917eea8c009c30d7f9917d5a341b9948
iuc
parents:
13
diff
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213 <test expect_num_outputs="2"> |
9
1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents:
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214 <param name="input1" value="mtcars.txt" ftype="tabular" /> |
1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents:
8
diff
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215 <section name="adv"> |
1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents:
8
diff
changeset
|
216 <conditional name="type_conditional"> |
1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents:
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217 <param name="type_options" value="points"/> |
1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents:
8
diff
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218 <conditional name="points"> |
1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents:
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diff
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219 <param name="pointoptions" value="default"/> |
1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents:
8
diff
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|
220 </conditional> |
1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents:
8
diff
changeset
|
221 </conditional> |
1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents:
8
diff
changeset
|
222 <conditional name="axis_text_customization"> |
1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents:
8
diff
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|
223 <param name="axis_customization" value="defined"/> |
1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents:
8
diff
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|
224 <param name="color" value="red"/> |
1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents:
8
diff
changeset
|
225 </conditional> |
1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents:
8
diff
changeset
|
226 </section> |
1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents:
8
diff
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|
227 <param name="additional_output_format" value="pdf" /> |
1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents:
8
diff
changeset
|
228 <output name="output2" file="ggplot_point_result2.pdf" compare="sim_size" /> |
1acf88921176
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
iuc
parents:
8
diff
changeset
|
229 </test> |
11
d0fc8b746d57
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 075aa3ab0ebc5eef83aac753a2cac7dffe2c6b0c
iuc
parents:
10
diff
changeset
|
230 <!-- Test lines option --> |
14
5298e06f14f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 6737c924917eea8c009c30d7f9917d5a341b9948
iuc
parents:
13
diff
changeset
|
231 <test expect_num_outputs="2"> |
11
d0fc8b746d57
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 075aa3ab0ebc5eef83aac753a2cac7dffe2c6b0c
iuc
parents:
10
diff
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232 <param name="input1" value="mtcars.txt" ftype="tabular" /> |
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233 <section name="adv"> |
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234 <conditional name="type_conditional"> |
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235 <param name="type_options" value="lines"/> |
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236 </conditional> |
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237 </section> |
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238 <param name="additional_output_format" value="pdf" /> |
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239 <output name="output2" file="ggplot_line_result1.pdf" compare="sim_size" /> |
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240 </test> |
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241 <!-- Test defined point options options--> |
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242 <test expect_num_outputs="2"> |
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243 <param name="input1" value="mtcars.txt" ftype="tabular" /> |
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244 <section name="adv"> |
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245 <conditional name="type_conditional"> |
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246 <param name="type_options" value="points"/> |
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247 <conditional name="points"> |
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248 <param name="pointoptions" value="defined"/> |
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249 <param name="size" value="2"/> |
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250 <param name="alpha" value="0.5"/> |
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251 <param name="pointcolor" value="gold"/> |
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252 <param name="shape" value="6"/> |
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253 </conditional> |
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254 </conditional> |
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255 <conditional name="axis_text_customization"> |
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256 <param name="axis_customization" value="defined"/> |
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257 <param name="color" value="red"/> |
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258 </conditional> |
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259 </section> |
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260 <param name="additional_output_format" value="pdf" /> |
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261 <output name="output2" file="ggplot_point_result3.pdf" ftype="pdf" compare="sim_size" /> |
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262 </test> |
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263 </tests> |
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264 <help><![CDATA[ |
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265 This tool will generate a scatterplot representing data from two groups/conditions. |
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266 |
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267 The input data should be in tabular format and the user can determine which groups (columns) to plot. |
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268 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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269 Multiple groups can be plotted on the same or multiple plots by providing a column with a group identifier under "advanced - plotting multiple groups". |
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270 |
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271 Feel free to explore the (many) advanced options to customize your plot. Galaxy makes this type optimization easy for the user! |
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272 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ggplot2 commit 4b44f8f834de15fd34e2fdc5e4aed282069f73af"
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273 The ouput is a pdf file with your scatterplot. The dimensions of this file can be modified under "advanced - output dimensions" |
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274 ]]></help> |
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275 <expand macro="citations"/> |
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276 </tool> |