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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
author ebi-gxa
date Wed, 03 Apr 2019 11:38:57 -0400
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c01a342be892 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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1 <tool id="scater_normalize" name="Scater Normalise" version="@TOOL_VERSION@+galaxy0">
c01a342be892 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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2 <description>expression values by library size in log2 scale</description>
c01a342be892 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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3 <macros>
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4 <import>scater_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 scater-normalize.R -i '${R_scater_qc}'
c01a342be892 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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9 #if $exprs_value:
c01a342be892 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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10 --exprs-values '$exprs_value'
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11 #end if
c01a342be892 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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12 #if $log_exprs_offset:
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13 --log-exprs-offset '$log_exprs_offset'
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14 #end if
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15 --return-log '$return_log'
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16 --centre-size-factors '$centre_size_factors'
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17 -o '$R_scater_normalize'
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18 ]]></command>
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19
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20 <inputs>
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21 <param name="R_scater_qc" type="data" format="rdata" label="SingleCellExperiment object"
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22 help="File name in which a serialized R SingleCellExperiment object where object matrix found."/>
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23
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24 <param name="exprs_value" argument="--exprs-values" type="text" optional="True" value="counts" label="Name of expression values"
c01a342be892 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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25 help="character string indicating which slot of the assayData from the SingleCellExperiment object should be used to compute log-transformed expression values. Valid options are counts, tpm, cpm and fpkm. Defaults to the first available value of the options in the order shown"/>
c01a342be892 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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26
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27 <param name="return_log" argument="--return-log" type="boolean" checked="true" label="Save normalized values in log scale"
c01a342be892 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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28 help="logical, should normalized values be returned on the log scale? Default is TRUE. If TRUE, output is stored as logcounts in the returned object; if FALSE output is stored as normcounts"/>
c01a342be892 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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29
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30 <param name="log_exprs_offset" argument="--log-exprs-offset" type="integer" optional="True" value="1" label="Pseudo counts to add when doing log transformation"
c01a342be892 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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31 help="scalar numeric value giving the offset to add when taking log2 of normalised values to return as expression values. If NULL, value is taken from log.exprs.offset if defined, otherwise 1."/>
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32
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33 <param name="centre_size_factors" argument="--centre-size-factors" type="boolean" checked="true" label="Save centred size factors"
c01a342be892 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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34 help="logical, should size factors centred at unity be stored in the returned object if exprs_values=counts, Defaults to TRUE. Regardless, centred size factors will always be used to calculate exprs from count data. This argument is ignored for other exprs_values, where no size factors are used or modified"/>
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35 </inputs>
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36
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37 <outputs>
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38 <data name="R_scater_normalize" format="rdata" label="${tool.name} on ${on_string}: serialized SingleCellExperiment object containing normalised expression values"/>
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39 </outputs>
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40
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41 <tests>
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42 <test>
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43 <param name="R_scater_qc" value="R_scater_qc.rds"/>
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44 <output name="R_scater_normalize" file="R_scater_normalize.rds"/>
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45 </test>
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46 </tests>
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47 <help><![CDATA[
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48 @HELP@
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49
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50 @VERSION_HISTORY@
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51 ]]></help>
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52 <expand macro="citations"/>
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53 </tool>