Mercurial > repos > ebi-gxa > scater_normalize
comparison scater-normalize.xml @ 0:c01a342be892 draft default tip
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
| author | ebi-gxa |
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| date | Wed, 03 Apr 2019 11:38:57 -0400 |
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| -1:000000000000 | 0:c01a342be892 |
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| 1 <tool id="scater_normalize" name="Scater Normalise" version="@TOOL_VERSION@+galaxy0"> | |
| 2 <description>expression values by library size in log2 scale</description> | |
| 3 <macros> | |
| 4 <import>scater_macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 scater-normalize.R -i '${R_scater_qc}' | |
| 9 #if $exprs_value: | |
| 10 --exprs-values '$exprs_value' | |
| 11 #end if | |
| 12 #if $log_exprs_offset: | |
| 13 --log-exprs-offset '$log_exprs_offset' | |
| 14 #end if | |
| 15 --return-log '$return_log' | |
| 16 --centre-size-factors '$centre_size_factors' | |
| 17 -o '$R_scater_normalize' | |
| 18 ]]></command> | |
| 19 | |
| 20 <inputs> | |
| 21 <param name="R_scater_qc" type="data" format="rdata" label="SingleCellExperiment object" | |
| 22 help="File name in which a serialized R SingleCellExperiment object where object matrix found."/> | |
| 23 | |
| 24 <param name="exprs_value" argument="--exprs-values" type="text" optional="True" value="counts" label="Name of expression values" | |
| 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"/> | |
| 26 | |
| 27 <param name="return_log" argument="--return-log" type="boolean" checked="true" label="Save normalized values in log scale" | |
| 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"/> | |
| 29 | |
| 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" | |
| 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."/> | |
| 32 | |
| 33 <param name="centre_size_factors" argument="--centre-size-factors" type="boolean" checked="true" label="Save centred size factors" | |
| 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"/> | |
| 35 </inputs> | |
| 36 | |
| 37 <outputs> | |
| 38 <data name="R_scater_normalize" format="rdata" label="${tool.name} on ${on_string}: serialized SingleCellExperiment object containing normalised expression values"/> | |
| 39 </outputs> | |
| 40 | |
| 41 <tests> | |
| 42 <test> | |
| 43 <param name="R_scater_qc" value="R_scater_qc.rds"/> | |
| 44 <output name="R_scater_normalize" file="R_scater_normalize.rds"/> | |
| 45 </test> | |
| 46 </tests> | |
| 47 <help><![CDATA[ | |
| 48 @HELP@ | |
| 49 | |
| 50 @VERSION_HISTORY@ | |
| 51 ]]></help> | |
| 52 <expand macro="citations"/> | |
| 53 </tool> |