comparison cummeRbund.xml @ 2:4bbfacecedd3 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f929353ffb0623f2218d7dec459c7da62f3b0d24"

1:aefbcaf15a94

<?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":
        $p.plot.smooth --x "$p.plot.x" --y "$p.plot.y" $p.plot.log10
        #if $p.plot.multiple_genes.multiple_genes_selector == "yes":
            --features $p.plot.multiple_genes.features --gene_selector
            #for gene in $p.plot.multiple_genes.genes:
                --genes ${gene.gene_id}
            #end for
        #end if
    #elif $p.plot.type == "maplot":
        --x "$p.plot.x" --y "$p.plot.y" $p.plot.count
    #elif $p.plot.type == "volcano":
        --x "$p.plot.x" --y "$p.plot.y"
        #if $p.plot.multiple_genes.multiple_genes_selector == "yes":
            --features $p.plot.multiple_genes.features --gene_selector
            #for gene in $p.plot.multiple_genes.genes:
                --genes ${gene.gene_id}
            #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":
        --features $p.plot.features --k $p.plot.k --iter_max $p.plot.iter_max
        #if len($p.plot.genes) > 0:
            #for gene in $p.plot.genes:
                --genes ${gene.gene_id}
            #end for
        #end if
    #elif $p.plot.type in [ "expressionplot", "expressionbarplot" ]:
        #if $p.plot.type == "expressionplot":
            $p.plot.draw_summary
        #end if
        --features $p.plot.features $p.plot.error_bars --genes ${p.plot.gene_id} $p.plot.replicates $p.plot.log10
    #end if
    #if $p.plot.type == "density":
        $p.plot.log10
    #end if
    > "${output}" 2>&1 ;
#end for
]]></command>
    <inputs>
        <param name="input_database" type="data" format="sqlite" label="Select backend database (sqlite)" />
        <repeat name="plots" title="Plots">

                    <param name="type" value="maplot" />
                    <param name="x" value="q1" />
                    <param name="y" value="q2" />
                </conditional>
            </repeat>
            <output name="output" ftype="txt" file="maplot.txt" lines_diff="2">
                <discovered_dataset designation="maplot-0" ftype="png" file="maplot.png" />
            </output>
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />

                    <param name="type" value="scatter" />
                    <param name="x" value="q1" />
                    <param name="y" value="q2" />
                </conditional>
            </repeat>
            <output name="output" ftype="txt" file="scatter.txt" lines_diff="2">
                <discovered_dataset designation="scatter-0" ftype="png" file="scatter.png" />
            </output>
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />

                <param name="height" value="960" />
                <conditional name="plot">
                    <param name="type" value="dispersion" />
                </conditional>
            </repeat>
            <output name="output" ftype="txt" file="dispersion.txt" lines_diff="2">
                <discovered_dataset designation="dispersion-0" ftype="png" file="dispersion.png" />
            </output>
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />

                <param name="height" value="960" />
                <conditional name="plot">
                    <param name="type" value="scatterMatrix" />
                </conditional>
            </repeat>
            <output name="output" ftype="txt" file="scatterMatrix.txt" lines_diff="2">
                <discovered_dataset designation="scatterMatrix-0" ftype="png" file="scatterMatrix.png" />
            </output>
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />

                <param name="height" value="960" />
                <conditional name="plot">
                    <param name="type" value="pca" />
                </conditional>
            </repeat>
            <output name="output" ftype="txt" file="pca.txt" lines_diff="2">
                <discovered_dataset designation="pca-0" ftype="png" file="pca.png" />
            </output>
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />

                    <param name="type" value="expressionplot" />
                    <param name="features" value="gene" />
                    <param name="gene_id" value="XLOC_000059" />
                </conditional>
            </repeat>
            <output name="output" ftype="txt" file="expressionplot.txt" lines_diff="2">
                <discovered_dataset designation="expressionplot-0" ftype="png" file="expressionplot.png" />
            </output>
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />

                    <param name="features" value="gene" />
                    <param name="type" value="expressionbarplot" />
                    <param name="gene_id" value="XLOC_000039" />
                </conditional>
            </repeat>
            <output name="output" ftype="txt" file="expressionbarplot.txt" lines_diff="2">
                <discovered_dataset designation="expressionbarplot-0" ftype="png" file="expressionbarplot.png" />
            </output>
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />

                    <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" />
            </output>
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />

                <param name="height" value="960" />
                <conditional name="plot">
                    <param name="type" value="density" />
                </conditional>
            </repeat>
            <output name="output" ftype="txt" file="density.txt" lines_diff="2">
                <discovered_dataset designation="density-0" ftype="png" file="density.png" />
            </output>
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />

                <param name="height" value="960" />
                <conditional name="plot">
                    <param name="type" value="dendrogram" />
                </conditional>
            </repeat>
            <output name="output" ftype="txt" file="dendrogram.txt" lines_diff="2">
                <discovered_dataset designation="dendrogram-0" ftype="png" file="dendrogram.png" />
            </output>
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />

                    <param name="type" value="volcano" />
                    <param name="x" value="q1" />
                    <param name="y" value="q2" />
                </conditional>
            </repeat>
            <output name="output" ftype="txt" file="volcano.txt" lines_diff="2">
                <discovered_dataset designation="volcano-0" ftype="png" file="volcano.png" />
            </output>
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />

                <param name="height" value="960" />
                <conditional name="plot">
                    <param name="type" value="boxplot" />
                </conditional>
            </repeat>
            <output name="output" ftype="txt" file="boxplot.txt" lines_diff="2">
                <discovered_dataset designation="boxplot-0" ftype="png" file="boxplot.png" />
            </output>
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />

                <param name="height" value="960" />
                <conditional name="plot">
                    <param name="type" value="fpkmSCV" />
                </conditional>
            </repeat>
            <output name="output" ftype="txt" file="fpkmSCV.txt" lines_diff="2">
                <discovered_dataset designation="fpkmSCV-0" ftype="png" file="fpkmSCV.png" />
            </output>
        </test>
    </tests>
    <help><![CDATA[

2:4bbfacecedd3

<?xml version="1.0"?>
<tool id="cummeRbund" name="cummeRbund" version="@TOOL_VERSION@+galaxy1">
    <description>visualize Cuffdiff output</description>
    <macros>
        <import>cummeRbund_macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="1">fonts-conda-ecosystem</requirement>
        <requirement type="package" version="1.0.4">r-argparse</requirement>
        <requirement type="package" version="3.4.1">r-base</requirement>
        <requirement type="package" version="@TOOL_VERSION@">bioconductor-cummerbund</requirement>
    </requirements>
    <code file="cummeRbund_options.py"/>
    <command detect_errors="aggressive">
<![CDATA[
#for i, p in enumerate($plots):
    Rscript --vanilla --slave '$__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":
        $p.plot.smooth --x "$p.plot.x" --y "$p.plot.y" $p.plot.log10
        #if $p.plot.multiple_genes.multiple_genes_selector == "yes":
            --features $p.plot.multiple_genes.features --gene_selector
            #for gene in $p.plot.multiple_genes.genes:
                --genes '$gene.gene_id'
            #end for
        #end if
    #elif $p.plot.type == "maplot":
        --x "$p.plot.x" --y "$p.plot.y" $p.plot.count
    #elif $p.plot.type == "volcano":
        --x "$p.plot.x" --y "$p.plot.y"
        #if $p.plot.multiple_genes.multiple_genes_selector == "yes":
            --features $p.plot.multiple_genes.features --gene_selector
            #for gene in $p.plot.multiple_genes.genes:
                --genes '$gene.gene_id'
            #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":
        --features $p.plot.features --k $p.plot.k --iter_max $p.plot.iter_max
        #if len($p.plot.genes) > 0:
            #for gene in $p.plot.genes:
                --genes '$gene.gene_id'
            #end for
        #end if
    #elif $p.plot.type in [ "expressionplot", "expressionbarplot" ]:
        #if $p.plot.type == "expressionplot":
            $p.plot.draw_summary
        #end if
        --features $p.plot.features $p.plot.error_bars --genes '$p.plot.gene_id' $p.plot.replicates $p.plot.log10
    #end if
    #if $p.plot.type == "density":
        $p.plot.log10
    #end if
    > '${output}' 2>&1 ;
#end for
]]></command>
    <inputs>
        <param name="input_database" type="data" format="sqlite" label="Select backend database (sqlite)" />
        <repeat name="plots" title="Plots">

                    <param name="type" value="maplot" />
                    <param name="x" value="q1" />
                    <param name="y" value="q2" />
                </conditional>
            </repeat>
            <output name="output" ftype="txt">
                <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
                <discovered_dataset designation="maplot-0" ftype="png" file="maplot.png" />
            </output>
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />

                    <param name="type" value="scatter" />
                    <param name="x" value="q1" />
                    <param name="y" value="q2" />
                </conditional>
            </repeat>
            <output name="output" ftype="txt">
                <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
                <discovered_dataset designation="scatter-0" ftype="png" file="scatter.png" />
            </output>
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />

                <param name="height" value="960" />
                <conditional name="plot">
                    <param name="type" value="dispersion" />
                </conditional>
            </repeat>
            <output name="output" ftype="txt">
                <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
                <discovered_dataset designation="dispersion-0" ftype="png" file="dispersion.png" />
            </output>
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />

                <param name="height" value="960" />
                <conditional name="plot">
                    <param name="type" value="scatterMatrix" />
                </conditional>
            </repeat>
            <output name="output" ftype="txt">
                <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
                <discovered_dataset designation="scatterMatrix-0" ftype="png" file="scatterMatrix.png" />
            </output>
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />

                <param name="height" value="960" />
                <conditional name="plot">
                    <param name="type" value="pca" />
                </conditional>
            </repeat>
            <output name="output" ftype="txt">
                <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
                <discovered_dataset designation="pca-0" ftype="png" file="pca.png" />
            </output>
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />

                    <param name="type" value="expressionplot" />
                    <param name="features" value="gene" />
                    <param name="gene_id" value="XLOC_000059" />
                </conditional>
            </repeat>
            <output name="output" ftype="txt">
                <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
                <discovered_dataset designation="expressionplot-0" ftype="png" file="expressionplot.png" />
            </output>
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />

                    <param name="features" value="gene" />
                    <param name="type" value="expressionbarplot" />
                    <param name="gene_id" value="XLOC_000039" />
                </conditional>
            </repeat>
            <output name="output" ftype="txt">
                <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
                <discovered_dataset designation="expressionbarplot-0" ftype="png" file="expressionbarplot.png" />
            </output>
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />

                    <repeat name="genes">
                        <param name="gene_id" value="XLOC_000037" />
                    </repeat>
                </conditional>
            </repeat>
            <output name="output" ftype="txt">
                <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
                <discovered_dataset designation="heatmap-0" ftype="png" file="heatmap.png" />
            </output>
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />

                <param name="height" value="960" />
                <conditional name="plot">
                    <param name="type" value="density" />
                </conditional>
            </repeat>
            <output name="output" ftype="txt">
                <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
                <discovered_dataset designation="density-0" ftype="png" file="density.png" />
            </output>
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />

                <param name="height" value="960" />
                <conditional name="plot">
                    <param name="type" value="dendrogram" />
                </conditional>
            </repeat>
            <output name="output" ftype="txt">
                <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
                <discovered_dataset designation="dendrogram-0" ftype="png" file="dendrogram.png" />
            </output>
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />

                    <param name="type" value="volcano" />
                    <param name="x" value="q1" />
                    <param name="y" value="q2" />
                </conditional>
            </repeat>
            <output name="output" ftype="txt">
                <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
                <discovered_dataset designation="volcano-0" ftype="png" file="volcano.png" />
            </output>
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />

                <param name="height" value="960" />
                <conditional name="plot">
                    <param name="type" value="boxplot" />
                </conditional>
            </repeat>
            <output name="output" ftype="txt">
                <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
                <discovered_dataset designation="boxplot-0" ftype="png" file="boxplot.png" />
            </output>
        </test>
        <test>
            <param name="input_database" value="cuffdiff_out.sqlite" ftype="sqlite" />

                <param name="height" value="960" />
                <conditional name="plot">
                    <param name="type" value="fpkmSCV" />
                </conditional>
            </repeat>
            <output name="output" ftype="txt">
                <assert_contents><has_text text="cummeRbund finished" /></assert_contents>
                <discovered_dataset designation="fpkmSCV-0" ftype="png" file="fpkmSCV.png" />
            </output>
        </test>
    </tests>
    <help><![CDATA[