comparison volcanoplot.xml @ 3:6d532d760950 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 16205b1cd782c5a4f7c08af7d4ee50dc5903418b

2:d1d39c72b755

<tool id="volcanoplot" name="Volcano Plot" version="0.0.2">
    <description>create a volcano plot</description>
    <requirements>
        <requirement type="package" version="3.0.0">r-ggplot2</requirement>
        <requirement type="package" version="0.8.0">r-ggrepel</requirement>
        <requirement type="package" version="0.7.6">r-dplyr</requirement>
        <requirement type="package" version="1.20.2">r-getopt</requirement>
    </requirements>
    <version_command><![CDATA[
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: ")
    ]]></version_command>

            -t $labels.top_num
        #end if
    #else
        -t 0
    #end if
    #if $plot_options.title:
        -T '$plot_options.title'
    #end if
    #if $plot_options.xlab:
        -X '$plot_options.xlab'
    #end if
    #if $plot_options.ylab:
        -Y '$plot_options.ylab'
    #end if
    #if $plot_options.legend:
        -L '$plot_options.legend'
    #end if
    -z '$plot_options.legend_labs'

            <when value="file">
                <param name="label_file" type="data" format="tabular" label="File of labels"/>
            </when>
        </conditional>
        <section name="plot_options" expanded="false" title="Plot Options">
            <param name="title" type="text" optional="True" label="Plot title"/>
            <param name="xlab" type="text" optional="True" label="Label for x axis"/>
            <param name="ylab" type="text" optional="True" label="Label for y axis"/>
            <param name="legend" type="text" optional="True" label="Label for Legend Title"/>
            <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"/>
        </section>
    </inputs>
    <outputs>

3:6d532d760950

<tool id="volcanoplot" name="Volcano Plot" version="0.0.3">
    <description>create a volcano plot</description>
    <requirements>
        <requirement type="package" version="3.1.0">r-ggplot2</requirement>
        <requirement type="package" version="0.8.0">r-ggrepel</requirement>
        <requirement type="package" version="0.7.8">r-dplyr</requirement>
        <requirement type="package" version="1.20.2">r-getopt</requirement>
    </requirements>
    <version_command><![CDATA[
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: ")
    ]]></version_command>

            -t $labels.top_num
        #end if
    #else
        -t 0
    #end if
    #if $plot_options.boxes:
        -b
    #end if
    #if $plot_options.title:
        -T '$plot_options.title'
    #end if
    #if $plot_options.xlab:
        -X '$plot_options.xlab'
    #end if
    #if $plot_options.ylab:
        -Y '$plot_options.ylab'
    #end if
    #if $plot_options.xmin:
        -m '$plot_options.xmin'
    #end if
    #if $plot_options.xmax:
        -M '$plot_options.xmax'
    #end if
    #if $plot_options.ymax:
        -W '$plot_options.ymax'
    #end if
    #if $plot_options.legend:
        -L '$plot_options.legend'
    #end if
    -z '$plot_options.legend_labs'

            <when value="file">
                <param name="label_file" type="data" format="tabular" label="File of labels"/>
            </when>
        </conditional>
        <section name="plot_options" expanded="false" title="Plot Options">
            <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"/>
            <param name="title" type="text" optional="True" label="Plot title"/>
            <param name="xlab" type="text" optional="True" label="Label for x axis"/>
            <param name="ylab" type="text" optional="True" label="Label for y axis"/>
            <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."/>
            <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."/>
            <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."/>
            <param name="legend" type="text" optional="True" label="Label for Legend Title"/>
            <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"/>
        </section>
    </inputs>
    <outputs>