comparison volcanoplot.xml @ 7:a363ba287b88 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 589795c240ea48accbb89cd0c3263f8eba301125

6:83c573f2e73c

<tool id="volcanoplot" name="Volcano Plot" version="0.0.5">
    <description>create a volcano plot</description>
    <edam_topics>
        <edam_topic>topic_0092</edam_topic>
    </edam_topics>
    <edam_operations>

                         max.overlaps = Inf,
                         show.legend = FALSE)
    #end if
#end if

#if not '$plot_options.title'
p <- p + ggtitle('$plot_options.title')
#end if

#if not '$plot_options.xlab'
p <- p + xlab('$plot_options.xlab')
#end if

#if not '$plot_options.ylab'
p <- p + ylab('$plot_options.ylab')
#end if

#if not '$plot_options.xmin' and '$plot_options.xmax'
p <- p + xlim('$plot_options.xmin', '$plot_options.xmax')
#end if

#if not '$plot_options.ymax'
p <- p + ylim(0, '$plot_options.ymax')
#end if

# Set legend title
#if not '$plot_options.legend'
p <- p + theme(legend.title = '$plot_options.legend')
#else
p <- p + theme(legend.title = element_blank())
#end if

# Print plot

        <param name="header" type="select" label="File has header?" help="Does the differentially expressed results file contain a header row. The tool can auto-detect by checking if the first row in the P value column is a number or not. Default: Auto-detect">
            <option value="auto" selected="True">Auto-detect</option>
            <option value="yes">Yes</option>
            <option value="no">No</option>
        </param>
        <param name="fdr_col" type="data_column" data_ref="input" label="FDR (adjusted P value)" />
        <param name="pval_col" type="data_column" data_ref="input" label="P value (raw)" />
        <param name="lfc_col" type="data_column" data_ref="input" label="Log Fold Change" />
        <param name="label_col" type="data_column" data_ref="input" label="Labels" />
        <param name="signif_thresh" type="float" max="1" value="0.05" label="Significance threshold" help="Default: 0.05"/>
        <param name="lfc_thresh" type="float" value="0" label="LogFC threshold to colour" help="Default: 0"/>
        <conditional name="labels">
            <param name="label_select" type="select" label="Points to label" help="Select to label significant points or input labels from file. Default: None">
                <option value="none" selected="True">None</option>

            <param name="lfc_thresh" value="0" />
            <param name="label_select" value="file"/>
            <param name="label_file" ftype="tabular" value="labels.tab" />
            <output name="plot">
                <assert_contents>
                    <has_size value= "933832" delta="1000" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="2">
            <!-- Ensure rscript output works -->

.. _Volcano plot: https://en.wikipedia.org/wiki/Volcano_plot_(statistics)
.. _blog post: https://gettinggeneticsdone.blogspot.com/2016/01/

    ]]></help>
    <citations>
    </citations>
</tool>

7:a363ba287b88

<tool id="volcanoplot" name="Volcano Plot" version="0.0.6" profile="20.09">
    <description>create a volcano plot</description>
    <edam_topics>
        <edam_topic>topic_0092</edam_topic>
    </edam_topics>
    <edam_operations>

                         max.overlaps = Inf,
                         show.legend = FALSE)
    #end if
#end if

#if $plot_options.title:
p <- p + ggtitle('$plot_options.title')
#end if

#if $plot_options.xlab:
p <- p + xlab('$plot_options.xlab')
#end if

#if $plot_options.ylab:
p <- p + ylab('$plot_options.ylab')
#end if

#if $plot_options.xmin and $plot_options.xmax:
p <- p + xlim($plot_options.xmin, $plot_options.xmax)
#end if

#if $plot_options.ymax:
p <- p + ylim(0, $plot_options.ymax)
#end if

# Set legend title
#if $plot_options.legend:
p <- p + guides(color = guide_legend(title = '$plot_options.legend'))
#else
p <- p + theme(legend.title = element_blank())
#end if

# Print plot

        <param name="header" type="select" label="File has header?" help="Does the differentially expressed results file contain a header row. The tool can auto-detect by checking if the first row in the P value column is a number or not. Default: Auto-detect">
            <option value="auto" selected="True">Auto-detect</option>
            <option value="yes">Yes</option>
            <option value="no">No</option>
        </param>
        <param name="fdr_col" type="data_column" data_ref="input" label="FDR (adjusted P value) column number" />
        <param name="pval_col" type="data_column" data_ref="input" label="P value (raw) column number" />
        <param name="lfc_col" type="data_column" data_ref="input" label="Log Fold Change column number" />
        <param name="label_col" type="data_column" data_ref="input" label="Labels column number" />
        <param name="signif_thresh" type="float" max="1" value="0.05" label="Significance threshold" help="Default: 0.05"/>
        <param name="lfc_thresh" type="float" value="0" label="LogFC threshold to colour" help="Default: 0"/>
        <conditional name="labels">
            <param name="label_select" type="select" label="Points to label" help="Select to label significant points or input labels from file. Default: None">
                <option value="none" selected="True">None</option>

            <param name="lfc_thresh" value="0" />
            <param name="label_select" value="file"/>
            <param name="label_file" ftype="tabular" value="labels.tab" />
            <output name="plot">
                <assert_contents>
                    <has_size value= "933830" delta="1000" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="2">
            <!-- Ensure rscript output works -->

.. _Volcano plot: https://en.wikipedia.org/wiki/Volcano_plot_(statistics)
.. _blog post: https://gettinggeneticsdone.blogspot.com/2016/01/

    ]]></help>
    <citations>
        <citation type="doi">doi.org/10.1007/978-3-319-24277-4</citation>
    </citations>
</tool>