comparison ggplot_point.xml @ 15:5a901c0cb006 draft

Uploaded

14:b342326db6dd

    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        Rscript ggplotpointscript.R --input "$input1" --title "$title" 
        --theme "${theme.theme_selector}" --xplot "$xplot" --yplot "$yplot" --scaling "$scaling.Plot_scaling" --points "$points.pointoptions" --dim "$dimensions.plotdim" --factor "$factor.factoring" --transform "$transformation.transform" --xlab "$xlab" --ylab "$ylab" 
        --axistitlecust "$axistitlecustomization.axistitlecust" --axistextcust "$axistextcustomization.axistextcust" 
        --plottitlecust "$plottitlecustomization.plottitlecust" --gridlinecust "$gridlinecustomization.gridlinecust" --output "Rplot.pdf"
        #if str( $factor.factoring ) == "Single":
            --factorcol ${factor.factorcol}

        #else:
           --factorcol=1
           --colors=irrelevant
           --colororder=1
        #end if
        #if str( $points.pointoptions ) == "Defined":
            --size ${points.size}
            --alpha ${points.alpha}
            --pointcolor ${points.pointcolor}
        #else:
           --size=1
           --alpha=1
           --pointcolor=black
        #end if
        #if str( $scaling.Plot_scaling ) == "Defined":
            --xaxismin=${scaling.xaxismin}
            --xaxismax=${scaling.xaxismax}
            --yaxismin=${scaling.yaxismin}
            --yaxismax=${scaling.yaxismax}

           --xaxismin=0
           --xaxismax=1
           --yaxismin=2
           --yaxismax=3
        #end if
        #if str( $axistitlecustomization.axistitlecust ) == "Defined":
            --axistitlesize ${axistitlecustomization.axistitlesize}
            --axistitlecolor ${axistitlecustomization.axistitlecolor}
            --axistitleface ${axistitlecustomization.axistitleface}
        #else:
            --axistitlesize=12
            --axistitlecolor=black
            --axistitleface=plain
        #end if
        #if str( $axistextcustomization.axistextcust ) == "Defined":
            --axistextsize ${axistextcustomization.axistextsize}
            --axistextcolor ${axistextcustomization.axistextcolor}
            --axistextface ${axistextcustomization.axistextface}
        #else:
            --axistextsize=12
            --axistextcolor=black
            --axistextface=plain
        #end if
        #if str( $plottitlecustomization.plottitlecust ) == "Defined":
            --plottitlesize ${plottitlecustomization.plottitlesize}
            --plottitlecolor ${plottitlecustomization.plottitlecolor}
            --plottitleface ${plottitlecustomization.plottitleface}
        #else:
            --plottitlesize=12
            --plottitlecolor=black
            --plottitleface=plain
        #end if
        #if str( $dimensions.plotdim ) == "Defined":
            --woutputdim ${dimensions.woutputdim}
            --houtputdim ${dimensions.houtputdim}
        #else:
           --woutputdim=7
           --houtputdim=7
        #end if
    ]]></command>
    <inputs>
        <param name="input1" type="data" format="tabular" label="Input (tabular format)" />
        <param name="xplot" type="integer" value="8" label="Column to plot on x-axis" />
        <param name="yplot" type="integer" value="9" label="Column to plot on y-axis" />

            <output name="output1" file="Rplot.pdf"/>
        </test>
    </tests>
    <help><![CDATA[
        This tool will generate a scatterplot representing data from two groups/conditions. 
        The input data should be in tabular format and the user can determine which groups (columns) to plot.
        Multiple groups can be plotted on the same or multiple plots by providing a column with a group identifier under "Advanced - plotting multiple groups".
        Feel free to explore the (many) advanced options to customize your plot. Galaxy makes this type optimization easy for the user!  
        The ouput is a pdf file with your scatterplot. The dimensions of this file can be modified under "Advanced - output dimensions"
        Please report issues at: https://github.com/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot
    ]]></help>
     <citations>
        <citation type="bibtex">
    @misc{renameTODO,

      title = {TODO},
      url = {http://docs.ggplot2.org/current/geom_point.html},
    }</citation>
        </citations>
    </tool>      

15:5a901c0cb006

    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        Rscript Rscript '${__tool_directory__}/ggplotpointscript.R' --input "$input1" --title "$title" 
        --theme "${theme.theme_selector}" --xplot "$xplot" --yplot "$yplot" --scaling "$scaling.Plot_scaling" --points "$points.pointoptions" --dim "$dimensions.plotdim" --factor "$factor.factoring" --transform "$transformation.transform" --xlab "$xlab" --ylab "$ylab" 
        --axistitlecust "$axistitlecustomization.axistitlecust" --axistextcust "$axistextcustomization.axistextcust" 
        --plottitlecust "$plottitlecustomization.plottitlecust" --gridlinecust "$gridlinecustomization.gridlinecust" --output "Rplot.pdf"
        #if str( $factor.factoring ) == "Single":
            --factorcol ${factor.factorcol}

        #else:
           --factorcol=1
           --colors=irrelevant
           --colororder=1
        #end if

        #if str( $points.pointoptions ) == "Defined":
            --size ${points.size}
            --alpha ${points.alpha}
            --pointcolor ${points.pointcolor}
        #else:
           --size=1
           --alpha=1
           --pointcolor=black
        #end if

        #if str( $scaling.Plot_scaling ) == "Defined":
            --xaxismin=${scaling.xaxismin}
            --xaxismax=${scaling.xaxismax}
            --yaxismin=${scaling.yaxismin}
            --yaxismax=${scaling.yaxismax}

           --xaxismin=0
           --xaxismax=1
           --yaxismin=2
           --yaxismax=3
        #end if

        #if str( $axistitlecustomization.axistitlecust ) == "Defined":
            --axistitlesize ${axistitlecustomization.axistitlesize}
            --axistitlecolor ${axistitlecustomization.axistitlecolor}
            --axistitleface ${axistitlecustomization.axistitleface}
        #else:
            --axistitlesize=12
            --axistitlecolor=black
            --axistitleface=plain
        #end if

        #if str( $axistextcustomization.axistextcust ) == "Defined":
            --axistextsize ${axistextcustomization.axistextsize}
            --axistextcolor ${axistextcustomization.axistextcolor}
            --axistextface ${axistextcustomization.axistextface}
        #else:
            --axistextsize=12
            --axistextcolor=black
            --axistextface=plain
        #end if

        #if str( $plottitlecustomization.plottitlecust ) == "Defined":
            --plottitlesize ${plottitlecustomization.plottitlesize}
            --plottitlecolor ${plottitlecustomization.plottitlecolor}
            --plottitleface ${plottitlecustomization.plottitleface}
        #else:
            --plottitlesize=12
            --plottitlecolor=black
            --plottitleface=plain
        #end if

        #if str( $dimensions.plotdim ) == "Defined":
            --woutputdim ${dimensions.woutputdim}
            --houtputdim ${dimensions.houtputdim}
        #else:
           --woutputdim=7
           --houtputdim=7
        #end if

    ]]></command>
    <inputs>
        <param name="input1" type="data" format="tabular" label="Input (tabular format)" />
        <param name="xplot" type="integer" value="8" label="Column to plot on x-axis" />
        <param name="yplot" type="integer" value="9" label="Column to plot on y-axis" />

            <output name="output1" file="Rplot.pdf"/>
        </test>
    </tests>
    <help><![CDATA[
        This tool will generate a scatterplot representing data from two groups/conditions. 

        The input data should be in tabular format and the user can determine which groups (columns) to plot.

        Multiple groups can be plotted on the same or multiple plots by providing a column with a group identifier under "Advanced - plotting multiple groups".

        Feel free to explore the (many) advanced options to customize your plot. Galaxy makes this type optimization easy for the user!  

        The ouput is a pdf file with your scatterplot. The dimensions of this file can be modified under "Advanced - output dimensions"




        Please report issues at: https://github.com/MoHeydarian/Galaxy-wrapper-for-ggplot2-scatterplot
    ]]></help>
     <citations>
        <citation type="bibtex">
    @misc{renameTODO,

      title = {TODO},
      url = {http://docs.ggplot2.org/current/geom_point.html},
    }</citation>
        </citations>
    </tool>