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comparison volcanoplot.xml @ 3:6d532d760950 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 16205b1cd782c5a4f7c08af7d4ee50dc5903418b
author iuc
date Tue, 12 Feb 2019 05:32:23 -0500
parents 7b7303fa20e3
children 73b8cb5bddcd
comparison
equal deleted inserted replaced
2:d1d39c72b755 3:6d532d760950
1 <tool id="volcanoplot" name="Volcano Plot" version="0.0.2"> 1 <tool id="volcanoplot" name="Volcano Plot" version="0.0.3">
2 <description>create a volcano plot</description> 2 <description>create a volcano plot</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.0.0">r-ggplot2</requirement> 4 <requirement type="package" version="3.1.0">r-ggplot2</requirement>
5 <requirement type="package" version="0.8.0">r-ggrepel</requirement> 5 <requirement type="package" version="0.8.0">r-ggrepel</requirement>
6 <requirement type="package" version="0.7.6">r-dplyr</requirement> 6 <requirement type="package" version="0.7.8">r-dplyr</requirement>
7 <requirement type="package" version="1.20.2">r-getopt</requirement> 7 <requirement type="package" version="1.20.2">r-getopt</requirement>
8 </requirements> 8 </requirements>
9 <version_command><![CDATA[ 9 <version_command><![CDATA[
10 echo $(R --version | grep version | grep -v GNU)", ggplot2 version" $(R --vanilla --slave -e "library(ggplot2); cat(sessionInfo()\$otherPkgs\$ggplot2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", ggrepel version" $(R --vanilla --slave -e "library(ggrepel); cat(sessionInfo()\$otherPkgs\$ggrepel\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", dplyr version" $(R --vanilla --slave -e "library(dplyr); cat(sessionInfo()\$otherPkgs\$dplyr\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ") 10 echo $(R --version | grep version | grep -v GNU)", ggplot2 version" $(R --vanilla --slave -e "library(ggplot2); cat(sessionInfo()\$otherPkgs\$ggplot2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", ggrepel version" $(R --vanilla --slave -e "library(ggrepel); cat(sessionInfo()\$otherPkgs\$ggrepel\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", dplyr version" $(R --vanilla --slave -e "library(dplyr); cat(sessionInfo()\$otherPkgs\$dplyr\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
11 ]]></version_command> 11 ]]></version_command>
27 -t $labels.top_num 27 -t $labels.top_num
28 #end if 28 #end if
29 #else 29 #else
30 -t 0 30 -t 0
31 #end if 31 #end if
32 #if $plot_options.boxes:
33 -b
34 #end if
32 #if $plot_options.title: 35 #if $plot_options.title:
33 -T '$plot_options.title' 36 -T '$plot_options.title'
34 #end if 37 #end if
35 #if $plot_options.xlab: 38 #if $plot_options.xlab:
36 -X '$plot_options.xlab' 39 -X '$plot_options.xlab'
37 #end if 40 #end if
38 #if $plot_options.ylab: 41 #if $plot_options.ylab:
39 -Y '$plot_options.ylab' 42 -Y '$plot_options.ylab'
43 #end if
44 #if $plot_options.xmin:
45 -m '$plot_options.xmin'
46 #end if
47 #if $plot_options.xmax:
48 -M '$plot_options.xmax'
49 #end if
50 #if $plot_options.ymax:
51 -W '$plot_options.ymax'
40 #end if 52 #end if
41 #if $plot_options.legend: 53 #if $plot_options.legend:
42 -L '$plot_options.legend' 54 -L '$plot_options.legend'
43 #end if 55 #end if
44 -z '$plot_options.legend_labs' 56 -z '$plot_options.legend_labs'
64 <when value="file"> 76 <when value="file">
65 <param name="label_file" type="data" format="tabular" label="File of labels"/> 77 <param name="label_file" type="data" format="tabular" label="File of labels"/>
66 </when> 78 </when>
67 </conditional> 79 </conditional>
68 <section name="plot_options" expanded="false" title="Plot Options"> 80 <section name="plot_options" expanded="false" title="Plot Options">
81 <param name="boxes" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Label Boxes" help="If this is set to Yes, the labels for the points will be in boxes. Default: Yes"/>
69 <param name="title" type="text" optional="True" label="Plot title"/> 82 <param name="title" type="text" optional="True" label="Plot title"/>
70 <param name="xlab" type="text" optional="True" label="Label for x axis"/> 83 <param name="xlab" type="text" optional="True" label="Label for x axis"/>
71 <param name="ylab" type="text" optional="True" label="Label for y axis"/> 84 <param name="ylab" type="text" optional="True" label="Label for y axis"/>
85 <param name="xmin" type="float" optional="True" label="Minimum value for x axis" help="To customise the x axis limits, specify both minimum and maximum values. Leave empty for automatic values."/>
86 <param name="xmax" type="float" optional="True" label="Maximum value for x axis" help="To customise the x axis limits, specify both minimum and maximum values. Leave empty for automatic values."/>
87 <param name="ymax" type="float" optional="True" label="Maximum value for y axis" help="To customise the y axis upper limit, specify the maximum value, the minimum will be 0. Leave empty for automatic value."/>
72 <param name="legend" type="text" optional="True" label="Label for Legend Title"/> 88 <param name="legend" type="text" optional="True" label="Label for Legend Title"/>
73 <param name="legend_labs" type="text" value="Down,Not Sig,Up" label="Labels for Legend" help="Labels in the legend can be specified. Default: Down,Not Sig,Up"/> 89 <param name="legend_labs" type="text" value="Down,Not Sig,Up" label="Labels for Legend" help="Labels in the legend can be specified. Default: Down,Not Sig,Up"/>
74 </section> 90 </section>
75 </inputs> 91 </inputs>
76 <outputs> 92 <outputs>