comparison dropletutils.xml @ 2:a8aa294401be draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit 4d89eb1eb951ef094d1f77c46824d9c38be4445b"

1:cfe1e6c28d95

<?xml version="1.0" encoding="utf-8"?>
<tool id="dropletutils" name="DropletUtils" version="@PACKAGE_VERSION@+@GALAXY_VERSION@" >
    <description>Utilities for handling droplet-based single-cell RNA-seq data</description>
    <macros>
        <token name="@PACKAGE_VERSION@" >1.2.1</token>
        <token name="@GALAXY_VERSION@" >2</token>
        <token name="@TXIN@">tenx.input</token>
        <token name="@TXOUT@">tenx.output</token>
        <xml name="test_dirin" >
            <conditional name="tenx_format">
                <param name="use" value="directory" />

                    <param name="use" type="select" label="Method" help="The DefaultDrops method calls cells according to the number of UMIs associated with each barcode as implemented by CellRanger. The EmptyDrops method identifies empty droplets using a smart ambient background model." >
                        <option value="defaultdrops" selected="true">DefaultDrops</option>
                        <option value="emptydrops">EmptyDrops</option>
                    </param>
                    <when value="defaultdrops">
                        <param name="expected" type="integer" min="10" value="3000" label="Expected Number of Cells" help="The expected number of cells in the sample." />
                        <param name="upperquant" type="float" min="0.1" max="1.0" value="0.99" label="Upper Quantile" help="The quantile of the top expected barcodes to consider." />
                        <param name="lowerprop" type="float" min="0.1" max="1.0" value="0.1" label="Lower Proportion" help="The fraction of molecules of the upper quantile that must be exceeded for a cell barcode to be detected." />
                    </when>
                    <when value="emptydrops">
                        <param name="lower" type="integer" min="10" value="100" label="Lower-bound Threshold" help="The lower-bound threshold of the total UMI count at which barcodes beneath this are assumed to be empty droplets." />
                        <param name="fdr_thresh" type="float" min="0" max="1" value="0.01" label="FDR Threshold" help="False Discovery Rate threshold at which droplets with significant deviations from the ambient profile are detected at this threshold." />
                    </when>
                </conditional>
                <param name="outformat" type="select" label="Format for output matrices">
                    <option value="directory" >Bundled (barcodes.tsv, genes.tsv, matrix.mtx)</option>
                    <option value="h5ad" selected="true" >AnnData/H5</option>
                    <option value="tsv">Tabular</option>
                </param>
            </when>
            <when value="barcode_rank">
                <param name="lower" type="integer" min="10" value="100" label="Lower Bound" help="Lower bound on the total UMI count, at or below which all barcodes are assumed to correspond to empty droplets."/>
            </when>
        </conditional>
        <param name="seed" type="integer" value="100" label="Random Seed" />
    </inputs>
    <outputs>

            <output name="fileout_h5ad" value="defs_emptydrops_150_0002.h5ad" compare="sim_size" delta="10" />
            <output name="table" >
                <assert_contents>
                    <has_n_columns n="9" />
                    <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" />
                    <has_line_matching expression="^1\sGGAAGAAGAA\s0\sNA\sNA\sNA\sNA\sNA\sNA" />
                    <has_line_matching expression="^11100\sGCTGAAGCAA\s71\sNA\sNA\sNA\sNA\sNA\sNA" />
                </assert_contents>
            </output>
            <output name="plot" value="defs_emptydrops_150_0002.png" compare="sim_size" delta="100" />
        </test>
        <!-- Other format input tests -->

            <output name="fileout_h5ad" value="defs_emptydrops_150_0002a.h5ad" compare="sim_size" delta="200" />
            <output name="table" >
                <assert_contents>
                    <has_n_columns n="9" />
                    <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" />
                    <has_line_matching expression="^1\sGGAAGAAGAA\s20\sNA\sNA\sNA\sNA\sNA\sNA" />
                    <has_line_matching expression="^11100\sGCTGAAGCAA\s203\s-222.833111872316\s9.99900009999e-05\sTRUE\s0.000126279506880773\sTRUE\sTRUE" />
                </assert_contents>
            </output>
            <output name="plot" value="defs_emptydrops_150_0002a.png" compare="sim_size" delta="100" />
        </test>
        <!-- Output a directory -->

2:a8aa294401be

<?xml version="1.0" encoding="utf-8"?>
<tool id="dropletutils" name="DropletUtils" version="@PACKAGE_VERSION@+@GALAXY_VERSION@" >
    <description>Utilities for handling droplet-based single-cell RNA-seq data</description>
    <macros>
        <token name="@PACKAGE_VERSION@" >1.2.1</token>
        <token name="@GALAXY_VERSION@" >3</token>
        <token name="@TXIN@">tenx.input</token>
        <token name="@TXOUT@">tenx.output</token>
        <xml name="test_dirin" >
            <conditional name="tenx_format">
                <param name="use" value="directory" />

                    <param name="use" type="select" label="Method" help="The DefaultDrops method calls cells according to the number of UMIs associated with each barcode as implemented by CellRanger. The EmptyDrops method identifies empty droplets using a smart ambient background model." >
                        <option value="defaultdrops" selected="true">DefaultDrops</option>
                        <option value="emptydrops">EmptyDrops</option>
                    </param>
                    <when value="defaultdrops">
                        <param name="expected" type="integer" min="1" value="3000" label="Expected Number of Cells" help="The expected number of cells in the sample." />
                        <param name="upperquant" type="float" min="0" max="1.0" value="0.99" label="Upper Quantile" help="The quantile of the top expected barcodes to consider." />
                        <param name="lowerprop" type="float" min="0" max="1.0" value="0.1" label="Lower Proportion" help="The fraction of molecules of the upper quantile that must be exceeded for a cell barcode to be detected." />
                    </when>
                    <when value="emptydrops">
                        <param name="lower" type="integer" min="1" value="100" label="Lower-bound Threshold" help="The lower-bound threshold of the total UMI count at which barcodes beneath this are assumed to be empty droplets." />
                        <param name="fdr_thresh" type="float" min="0" max="1" value="0.01" label="FDR Threshold" help="False Discovery Rate threshold at which droplets with significant deviations from the ambient profile are detected at this threshold. If set to 0, the threshold is ignored." />
                    </when>
                </conditional>
                <param name="outformat" type="select" label="Format for output matrices">
                    <option value="directory" >Bundled (barcodes.tsv, genes.tsv, matrix.mtx)</option>
                    <option value="h5ad" selected="true" >AnnData/H5</option>
                    <option value="tsv">Tabular</option>
                </param>
            </when>
            <when value="barcode_rank">
                <param name="lower" type="integer" min="1" value="100" label="Lower Bound" help="Lower bound on the total UMI count, at or below which all barcodes are assumed to correspond to empty droplets."/>
            </when>
        </conditional>
        <param name="seed" type="integer" value="100" label="Random Seed" />
    </inputs>
    <outputs>

            <output name="fileout_h5ad" value="defs_emptydrops_150_0002.h5ad" compare="sim_size" delta="10" />
            <output name="table" >
                <assert_contents>
                    <has_n_columns n="9" />
                    <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" />
                    <has_line_matching expression="^994\sGGCATTACAA\s338\s-246.922772388055\s9.99900009999e-05\sTRUE\s9.99900009999e-05\sTRUE\sTRUE" />
                    <has_line_matching expression="^998\sCATGAAGCAA\s151\s-166.644236503983\s9.99900009999e-05\sTRUE\s9.99900009999e-05\sTRUE\sTRUE" />
                </assert_contents>
            </output>
            <output name="plot" value="defs_emptydrops_150_0002.png" compare="sim_size" delta="100" />
        </test>
        <!-- Other format input tests -->

            <output name="fileout_h5ad" value="defs_emptydrops_150_0002a.h5ad" compare="sim_size" delta="200" />
            <output name="table" >
                <assert_contents>
                    <has_n_columns n="9" />
                    <has_line_matching expression="^\sbar.names\sTotal\sLogProb\sPValue\sLimited\sFDR\sis.Cell\sis.CellAndLimited" />
                    <has_line_matching expression="^1100\sCCGGAAGCAA\s169\s-198.117943099773\s9.99900009999e-05\sTRUE\s0.000126279506880773\sTRUE\sTRUE" />
                    <has_line_matching expression="^1114\sTCCGAAGCAA\s182\s-196.181449214729\s9.99900009999e-05\sTRUE\s0.000126279506880773\sTRUE\sTRUE" />
                </assert_contents>
            </output>
            <output name="plot" value="defs_emptydrops_150_0002a.png" compare="sim_size" delta="100" />
        </test>
        <!-- Output a directory -->