comparison cummeRbund.xml @ 5:78fcfc04fcfe draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f3f0bef4a450aafab3c6b05a27647471f93b22f3

4:ba8fde59843d

<?xml version="1.0"?>
<tool id="cummeRbund" name="cummeRbund" version="1.0.1">
    <description>visualize Cuffdiff output</description>
    <requirements>
        <requirement type="set_environment">CUMMERBUND_SCRIPT_PATH</requirement>
        <requirement type="package" version="3.1.2">R</requirement>
        <requirement type="package" version="2.8.2">cummeRbund</requirement>
    </requirements>
    <expand macro="stdio" />
    <macros>
        <import>cummeRbund_macros.xml</import>
    </macros>
    <code file="cummeRbund_options.py"/>
    <command>
<![CDATA[
#for i, p in enumerate($plots):
    R --vanilla --no-save -f \$CUMMERBUND_SCRIPT_PATH/cummeRbund.R --args
    --input "${input_database}" --width $p.width --height $p.height --type "${p.plot.type}"
    --outfile plot-${p.plot.type}-${i}.png
    #if $p.plot.type in ["density", "boxplot", "mds", "pca", "dendrogram"]:
        $p.plot.replicates
    #elif $p.plot.type == "scatter":

            #end for
        #end if
    #elif $p.plot.type == "heatmap":
        --clustering "$p.plot.clustering" $p.plot.labcol $p.plot.labrow $p.plot.border --features $p.plot.features $p.plot.log10
        #if len($p.plot.genes) > 0:
            #for gene in $p.plot.genes:
                --genes ${gene.gene_id}
            #end for
        #end if
    #elif $p.plot.type == "cluster":

                        <option value="column">Column</option>
                        <option value="both" selected="true">Both</option>
                        <option value="none">None</option>
                    </param>
                    <param name="labcol" type="boolean" truevalue="--labcol" falsevalue="" checked="True" label="Display column labels?"/>
                    <param name="labrow" type="boolean" truevalue="--labrow" falsevalue="" checked="True" label="Display column labels?"/>
                    <param name="border" type="boolean" truevalue="--border" falsevalue="" checked="False" label="Draw border around plot?"/>
                    <expand macro="log10_checkbox" />
                </when>
                <when value="cluster">
                    <expand macro="features_selector" />

                <param name="width" value="1280" />
                <param name="height" value="960" />
                <conditional name="plot">
                    <param name="type" value="heatmap" />
                    <repeat name="genes">
                        <param name="gene_id" value="XLOC_000078" />
                    </repeat>
                </conditional>
            </repeat>
            <output name="output" ftype="txt" file="heatmap.txt" lines_diff="2">
                <discovered_dataset designation="heatmap-0" ftype="png" file="heatmap.png" />

    <help><![CDATA[
This tool allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.

------

Based on the `cummeRbund wrapper <http://toolshed.bx.psu.edu/view/jjohnson/cummerbund>`_ written by James E. Johnson of the Minnesota Supercomputing Institute.
    ]]></help>
    <citations>
        <citation type="doi">doi:10.1038/nprot.2012.016</citation>
    </citations>
</tool>

5:78fcfc04fcfe

<?xml version="1.0"?>
<tool id="cummeRbund" name="cummeRbund" version="2.16.0">
    <description>visualize Cuffdiff output</description>
    <macros>
        <import>cummeRbund_macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="1.0.1">r-argparse</requirement>
        <requirement type="package" version="2.16.0">bioconductor-cummerbund</requirement>
    </requirements>
    <code file="cummeRbund_options.py"/>
    <command detect_errors="aggressive">
<![CDATA[
#for i, p in enumerate($plots):
    Rscript $__tool_directory__/cummeRbund.R
    --input "${input_database}" --width $p.width --height $p.height --type "${p.plot.type}"
    --outfile plot-${p.plot.type}-${i}.png
    #if $p.plot.type in ["density", "boxplot", "mds", "pca", "dendrogram"]:
        $p.plot.replicates
    #elif $p.plot.type == "scatter":

            #end for
        #end if
    #elif $p.plot.type == "heatmap":
        --clustering "$p.plot.clustering" $p.plot.labcol $p.plot.labrow $p.plot.border --features $p.plot.features $p.plot.log10
        #if len($p.plot.genes) > 0:
            --gene_selector
            #for gene in $p.plot.genes:
                --genes ${gene.gene_id}
            #end for
        #end if
    #elif $p.plot.type == "cluster":

                        <option value="column">Column</option>
                        <option value="both" selected="true">Both</option>
                        <option value="none">None</option>
                    </param>
                    <param name="labcol" type="boolean" truevalue="--labcol" falsevalue="" checked="True" label="Display column labels?"/>
                    <param name="labrow" type="boolean" truevalue="--labrow" falsevalue="" checked="True" label="Display row labels?"/>
                    <param name="border" type="boolean" truevalue="--border" falsevalue="" checked="False" label="Draw border around plot?"/>
                    <expand macro="log10_checkbox" />
                </when>
                <when value="cluster">
                    <expand macro="features_selector" />

                <param name="width" value="1280" />
                <param name="height" value="960" />
                <conditional name="plot">
                    <param name="type" value="heatmap" />
                    <repeat name="genes">
                        <param name="gene_id" value="XLOC_000030" />
                    </repeat>
                    <repeat name="genes">
                        <param name="gene_id" value="XLOC_000037" />
                    </repeat>
                </conditional>
            </repeat>
            <output name="output" ftype="txt" file="heatmap.txt" lines_diff="2">
                <discovered_dataset designation="heatmap-0" ftype="png" file="heatmap.png" />

    <help><![CDATA[
This tool allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.

------

Based on the `cummeRbund wrapper <https://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund>`_ written by James E. Johnson of the Minnesota Supercomputing Institute.
    ]]></help>
    <citations>
        <citation type="doi">doi:10.1038/nprot.2012.016</citation>
    </citations>
</tool>