comparison dropletutils.xml @ 6:8855361fcfc5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dropletutils/ commit ed0625fe59342d14a08745996e3e32c6f922a738"

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" />

                <param name="input_genes" value="in_genes.tsv" />
            </conditional>
        </xml>
    </macros>
    <requirements>
        <requirement type="package" version="@PACKAGE_VERSION@">bioconductor-dropletutils</requirement>
        <requirement type="package" version="1.2_17" >r-matrix</requirement>
        <requirement type="package" version="1.10.1" >bioconductor-scater</requirement>
        <requirement type="package" version="1">fonts-conda-ecosystem</requirement>
    </requirements>
    <version_command><![CDATA[
    Rscript -e 'packageVersion("DropletUtils")' | grep -oP '\d\.\d\.\d'
    ]]>

    ]]>
    </command>
    <configfiles>
        <configfile name="droplet_conf" >
## defaults
empty.fdr_threshold = 0.01
eparams=formals(emptyDrops)
dparams=formals(defaultDrops)
bparams=formals(barcodeRanks)

## File params
in.type='$tenx_format.use'
out.type=NULL

files=list()
files\$table='$table'
files\$plot='$plot'
files\$out=NULL

dparams\$upper.quant=as.numeric('$operation.method.upperquant')
dparams\$lower.prop=as.numeric('$operation.method.lowerprop')
    #else if str($operation.method.use) == 'emptydrops':
do.method="emptyDrops"
eparams\$lower=as.integer('$operation.method.lower')
empty.fdr_threshold=as.numeric('$operation.method.fdr_thresh')
    #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':

            <filter>operation['use']=='filter' and operation['method']['use']=="emptydrops"</filter>
        </data>
    </outputs>
    <tests>
        <!-- Directory input tests -->
        <!-- ::: 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>

                    <has_text_matching expression="GENE50\s4\s0\s0\s0\s0\s5\s11\s8\s5" />
                    <has_text_matching expression="GENE100\s6\s3\s5\s0\s0\s16\s31\s15\s26" />
                </assert_contents>
            </output>
        </test>
        <!-- :: Barcode Ranks -->
        <test expect_num_outputs="1">
            <expand macro="test_dirin" />
            <conditional name="operation">
                <param name="use" value="barcode_rank" />
                <param name="lower" value="120" />
            </conditional>
            <output name="plot" value="defs_barcoderankings.png" compare="sim_size" delta="400"/>
        </test>
        <!-- ::: 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">

            </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" />
                    <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="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">

            </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" />
                    <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="400" />
        </test>
        <!-- Output a directory -->

6:8855361fcfc5

<?xml version="1.0" encoding="utf-8"?>
<tool id="dropletutils" name="DropletUtils" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
    <description>Utilities for handling droplet-based single-cell RNA-seq data</description>
    <xrefs>
        <xref type="bio.tools">dropletutils</xref>
    </xrefs>
    <edam_topics>
        <edam_topic>topic_0203</edam_topic>
        <edam_topic>topic_3168</edam_topic>
        <edam_topic>topic_3170</edam_topic>
        <edam_topic>topic_3308</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_1812</edam_operation>
        <edam_operation>operation_3200</edam_operation>
    </edam_operations>
    <macros>
        <token name="@TOOL_VERSION@">1.10.0</token>
        <token name="@VERSION_SUFFIX@">0</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="input_genes" value="in_genes.tsv" />
            </conditional>
        </xml>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">bioconductor-dropletutils</requirement>
        <requirement type="package" version="1.18.0" >bioconductor-scater</requirement>
        <requirement type="package" version="4.0">r-base</requirement>
        <requirement type="package" version="1.2_18">r-matrix</requirement>
        <requirement type="package" version="1">fonts-conda-ecosystem</requirement>
    </requirements>
    <version_command><![CDATA[
    Rscript -e 'packageVersion("DropletUtils")' | grep -oP '\d\.\d\.\d'
    ]]>

    ]]>
    </command>
    <configfiles>
        <configfile name="droplet_conf" >
## defaults
empty_fdr_threshold = 0.01
eparams = formals(emptyDrops)
dparams = formals(defaultDrops)
bparams = formals(barcodeRanks)

## File params
intype='$tenx_format.use'
outtype=NULL

files=list()
files\$table='$table'
files\$plot='$plot'
files\$out=NULL

dparams\$upper.quant=as.numeric('$operation.method.upperquant')
dparams\$lower.prop=as.numeric('$operation.method.lowerprop')
    #else if str($operation.method.use) == 'emptydrops':
do.method="emptyDrops"
eparams\$lower=as.integer('$operation.method.lower')
empty_fdr_threshold=as.numeric('$operation.method.fdr_thresh')
    #end if

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

            <filter>operation['use']=='filter' and operation['method']['use']=="emptydrops"</filter>
        </data>
    </outputs>
    <tests>
        <!-- Directory input tests -->
        <test expect_num_outputs="1">
            <!-- ::: Default Drops -->
            <expand macro="test_dirin" />
            <conditional name="operation">
                <param name="use" value="filter" />
                <param name="outformat" value="h5" /><!-- H5 -->
            </conditional>

                    <has_text_matching expression="GENE50\s4\s0\s0\s0\s0\s5\s11\s8\s5" />
                    <has_text_matching expression="GENE100\s6\s3\s5\s0\s0\s16\s31\s15\s26" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <!-- :: Barcode Ranks -->
            <expand macro="test_dirin" />
            <conditional name="operation">
                <param name="use" value="barcode_rank" />
                <param name="lower" value="120" />
            </conditional>
            <output name="plot" value="defs_barcoderankings.png" compare="sim_size" delta="600"/>
        </test>
        <test expect_num_outputs="3">
            <!-- ::: Empty Drops -->
            <expand macro="test_dirin" />
            <conditional name="operation">
                <param name="use" value="filter" />
                <param name="outformat" value="h5" />
                <conditional name="method">

            </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\.(.*TRUE){3}$" />
                    <has_line_matching expression="^998\sCATGAAGCAA\s151\s-166\.(.*TRUE){3}$" />
                </assert_contents>
            </output>
            <output name="plot" value="defs_emptydrops_150_0002.png" compare="sim_size" delta="400" />
        </test>
        <!-- Other format input tests -->
        <test expect_num_outputs="3">
            <!-- ::: Empty Drops, same as above but input is h5 -->
            <conditional name="tenx_format" >
                <param name="use" value="h5" />
                <param name="input" value="in_matrix.h5" />
            </conditional>
            <conditional name="operation">

            </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\.(.*TRUE){3}$" />
                    <has_line_matching expression="^1114\sTCCGAAGCAA\s182\s-196\.(.*TRUE){3}$" />
                </assert_contents>
            </output>
            <output name="plot" value="defs_emptydrops_150_0002a.png" compare="sim_size" delta="400" />
        </test>
        <!-- Output a directory -->