comparison dropletutils.xml @ 5:cdf4443d5625 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ea9a67b5711b53fb911a0c50b6b49eb9db2366a7"

4:1797cbe967d1

<?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@" >5</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" />

    #end if

out.type='$operation.outformat'
    #if str($operation.outformat) == 'directory':
files\$out='@TXOUT@'
    #else if str($operation.outformat) == 'h5ad':
files\$out='$fileout_h5ad'
    #else if str($operation.outformat) == 'tsv':
files\$out='$fileout_tsv'
    #end if

#else if str($operation.use) == 'barcode_rank':

    </configfiles>
    <inputs>
        <conditional name="tenx_format">
            <param name="use" type="select" label="Format for the input matrix">
                <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 value="directory">
                <param name="input" type="data" format="mtx,txt" label="Count Data"/>
                <param name="input_genes" type="data" format="tabular,tsv,txt" label="Genes List"/>
                <param name="input_barcodes" type="data" format="tabular,tsv,txt" label="Barcodes List"/>
            </when>
            <when value="h5ad">
                <param name="input" type="data" format="h5ad" label="Count Data"/>
            </when>
            <when value="tsv">
                <param name="input" type="data" format="tabular,tsv" label="Count Data" help="The first column must contain gene names, and the first row must contain barcode identifiers." />
            </when>
        </conditional>

                        <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."/>

    </inputs>
    <outputs>
        <data name="fileout_tsv" format="tsv" label="${tool.name} Count Matrix on ${on_string}">
            <filter>operation['use']=='filter' and operation['outformat'] == 'tsv' </filter>
        </data>
        <data name="fileout_h5ad" format="h5ad" label="${tool.name} AnnData on ${on_string}">
            <filter>operation['use']=='filter' and operation['outformat'] == 'h5ad'</filter>
        </data>
        <data name="barcodes_out" format="tsv" from_work_dir="@TXOUT@/barcodes.tsv" label="${tool.name} 10X Barcodes on ${on_string}" >
            <filter>operation['use']=='filter' and operation['outformat'] == 'directory'</filter>
        </data>
        <data name="genes_out" format="tsv" from_work_dir="@TXOUT@/genes.tsv" label="${tool.name} 10X Genes on ${on_string}" >

        <!-- ::: Default Drops -->
        <test expect_num_outputs="1">
            <expand macro="test_dirin" />
            <conditional name="operation">
                <param name="use" value="filter" />
                <param name="outformat" value="h5ad" /><!-- H5AD -->
            </conditional>
            <output name="fileout_h5ad" value="defs_defaultdrops.h5ad" compare="sim_size" delta="10" />
        </test>
        <test expect_num_outputs="1">
            <expand macro="test_dirin" />
            <conditional name="operation">
                <param name="use" value="filter" />

        <!-- ::: Empty Drops -->
        <test expect_num_outputs="3">
            <expand macro="test_dirin" />
            <conditional name="operation">
                <param name="use" value="filter" />
                <param name="outformat" value="h5ad" />
                <conditional name="method">
                    <param name="use" value="emptydrops" />
                    <param name="lower" value="150" />
                    <param name="fdr_thresh" value="0.02" />
                </conditional>
            </conditional>
            <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" />

                </assert_contents>
            </output>
            <output name="plot" value="defs_emptydrops_150_0002.png" compare="sim_size" delta="400" />
        </test>
        <!-- Other format input tests -->
        <!-- ::: Empty Drops, same as above but input is h5ad -->
        <test expect_num_outputs="3">
            <conditional name="tenx_format" >
                <param name="use" value="h5ad" />
                <param name="input" value="in_matrix.h5ad" />
            </conditional>
            <conditional name="operation">
                <param name="use" value="filter" />
                <param name="outformat" value="h5ad" />
                <conditional name="method">
                    <param name="use" value="emptydrops" />
                    <param name="lower" value="150" />
                    <param name="fdr_thresh" value="0.02" />
                </conditional>
            </conditional>
            <output name="fileout_h5ad" value="defs_emptydrops_150_0002a.h5ad" compare="sim_size" delta="400" />
            <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" />

5:cdf4443d5625

<?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@" >galaxy6</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" />

    #end if

out.type='$operation.outformat'
    #if str($operation.outformat) == 'directory':
files\$out='@TXOUT@'
    #else if str($operation.outformat) == 'h5':
files\$out='$fileout_h5'
    #else if str($operation.outformat) == 'tsv':
files\$out='$fileout_tsv'
    #end if

#else if str($operation.use) == 'barcode_rank':

    </configfiles>
    <inputs>
        <conditional name="tenx_format">
            <param name="use" type="select" label="Format for the input matrix">
                <option value="directory" >Bundled (barcodes.tsv, genes.tsv, matrix.mtx)</option>
                <option value="h5" selected="true" >H5</option>
                <option value="tsv">Tabular</option>
            </param>
            <when value="directory">
                <param name="input" type="data" format="mtx,txt" label="Count Data"/>
                <param name="input_genes" type="data" format="tabular,tsv,txt" label="Genes List"/>
                <param name="input_barcodes" type="data" format="tabular,tsv,txt" label="Barcodes List"/>
            </when>
            <when value="h5">
                <param name="input" type="data" format="h5" label="Count Data"/>
            </when>
            <when value="tsv">
                <param name="input" type="data" format="tabular,tsv" label="Count Data" help="The first column must contain gene names, and the first row must contain barcode identifiers." />
            </when>
        </conditional>

                        <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="h5" selected="true" >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."/>

    </inputs>
    <outputs>
        <data name="fileout_tsv" format="tsv" label="${tool.name} Count Matrix on ${on_string}">
            <filter>operation['use']=='filter' and operation['outformat'] == 'tsv' </filter>
        </data>
        <data name="fileout_h5" format="h5" label="${tool.name} H5 Matrix on ${on_string}">
            <filter>operation['use']=='filter' and operation['outformat'] == 'h5'</filter>
        </data>
        <data name="barcodes_out" format="tsv" from_work_dir="@TXOUT@/barcodes.tsv" label="${tool.name} 10X Barcodes on ${on_string}" >
            <filter>operation['use']=='filter' and operation['outformat'] == 'directory'</filter>
        </data>
        <data name="genes_out" format="tsv" from_work_dir="@TXOUT@/genes.tsv" label="${tool.name} 10X Genes on ${on_string}" >

        <!-- ::: Default Drops -->
        <test expect_num_outputs="1">
            <expand macro="test_dirin" />
            <conditional name="operation">
                <param name="use" value="filter" />
                <param name="outformat" value="h5" /><!-- H5 -->
            </conditional>
            <output name="fileout_h5" value="defs_defaultdrops.h5" compare="sim_size" delta="10" />
        </test>
        <test expect_num_outputs="1">
            <expand macro="test_dirin" />
            <conditional name="operation">
                <param name="use" value="filter" />

        <!-- ::: Empty Drops -->
        <test expect_num_outputs="3">
            <expand macro="test_dirin" />
            <conditional name="operation">
                <param name="use" value="filter" />
                <param name="outformat" value="h5" />
                <conditional name="method">
                    <param name="use" value="emptydrops" />
                    <param name="lower" value="150" />
                    <param name="fdr_thresh" value="0.02" />
                </conditional>
            </conditional>
            <output name="fileout_h5" value="defs_emptydrops_150_0002.h5" 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" />

                </assert_contents>
            </output>
            <output name="plot" value="defs_emptydrops_150_0002.png" compare="sim_size" delta="400" />
        </test>
        <!-- Other format input tests -->
        <!-- ::: Empty Drops, same as above but input is h5 -->
        <test expect_num_outputs="3">
            <conditional name="tenx_format" >
                <param name="use" value="h5" />
                <param name="input" value="in_matrix.h5" />
            </conditional>
            <conditional name="operation">
                <param name="use" value="filter" />
                <param name="outformat" value="h5" />
                <conditional name="method">
                    <param name="use" value="emptydrops" />
                    <param name="lower" value="150" />
                    <param name="fdr_thresh" value="0.02" />
                </conditional>
            </conditional>
            <output name="fileout_h5" value="defs_emptydrops_150_0002a.h5" compare="sim_size" delta="400" />
            <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" />