Mercurial > repos > ebi-gxa > sc3_prepare
diff sc3-prepare.xml @ 0:9a2b61bfdaa9 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 11:30:49 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sc3-prepare.xml Wed Apr 03 11:30:49 2019 -0400 @@ -0,0 +1,114 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="sc3_prepare" name="SC3 Prepare" version="@TOOL_VERSION@+galaxy0"> + <description>a sc3 SingleCellExperiment object</description> + <macros> + <import>sc3-macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ +sc3-sc3-prepare.R -i '${scater_log}' -o '${sc3_prepared}' -t 1 + +#if $gene_filter.use: + -f TRUE + -p '${gene_filter.pct_dropout_min}' + -q '${gene_filter.pct_dropout_max}' +#end if +#if $d_region_min: + -d '${d_region_min}' +#end if +#if $d_region_max: + -d '${d_region_max}' +#end if +#if $svm_num_cells: + -n '${svm_num_cells}' +#end if +#if $svm_train_inds: + -r '${svm_train_inds}' +#end if +#if $svm_max: + -m '${svm_max}' +#end if +#if $seed: + -s '${seed}' +#end if +#if $kmeans_nstart: + -k '${kmeans_nstart}' +#end if +#if $kmeans_iter_max: + -a '${kmeans_iter_max}' +#end if + + ]]></command> + + <inputs> + <param name="scater_log" type="data" format="rdata" label="Serialised SingleCellExperiment object normalised by scater"/> + + <conditional name="gene_filter"> + <param name="use" argument="--gene-filter" type="boolean" label="Perform gene filtering?" + help="A boolean variable which defines whether to perform gene filtering before SC3 clustering."/> + <when value="true"> + <param name="pct_dropout_min" argument="--pct-dropout-min" type="integer" value="10" label="Minimum percent of dropouts" + help="An integer value. Genes with percent of dropouts smaller than this value are filtered out before clustering."/> + <param name="pct_dropout_max" argument="--pct-dropout-max" type="integer" value="90" label="Maximum percent of dropouts" + help="An integer value. Genes with percent of dropouts larger than this value are filtered out before clustering."/> + </when> + <when value="false"/> + </conditional> + + <param name="d_region_min" argument="--d-region-min" type="float" value="0.04" optional="true" + label="Minimum number of eigenvectors used for kmeans clustering as a fraction of the total number of cells"/> + + <param name="d_region_max" argument="--d-region-max" type="float" value="0.07" optional="true" + label="Maximum number of eigenvectors used for kmeans clustering as a fraction of the total number of cells"/> + + <param name="svm_num_cells" argument="--svm-num-cells" type="integer" optional="true" + label="Number of randomly selected training cells to be used for SVM prediction."/> + + <param name="svm_train_inds" argument="--svm-train-inds" type="data" format="txt" optional="true" + label="Text file with one integer per line defining indices of training cells that should be used for SVM training"/> + + <param name="svm_max" argument="--svm-max" type="integer" value="5000" + label="The number of cells below which SVM are not run"/> + + <param name="seed" argument="--rand-seed" type="integer" value="1" optional="true" label="Seed of the random number generator" + help="SC3 is a stochastic method, so setting the rand_seed to a fixed values can be used for reproducibility purposes."/> + + <param name="kmeans_nstart" argument="--kmeans-nstart" type="integer" optional="true" label="Number of random starts for kmeans" + help="When unspecified, default to 1000 for up to 2000 cells and 50 for more than 2000 cells."/> + + <param name="kmeans_iter_max" argument="--kmeans-iter-max" type="integer" optional="true" label="Maximum number of iterations for kmeans" + help="When unspecified, default to 1e+9."/> + </inputs> + + <outputs> + <data name="sc3_prepared" format="rdata" label="${tool.name} on ${on_string}: serialised sc3 SingleCellExperiment object"/> + </outputs> + + <tests> + <test> + <param name="scater_log" value="scater_log.rdata"/> + <output name="sc3_prepared" file="sc3_prepared.rdata"/> + </test> + </tests> + + <help><![CDATA[ + +================================================================================== +This function prepares an object of SingleCellExperiment class for SC3 clustering. +================================================================================== +It creates and populates the following items of the sc3 slot of the metadata(object): + +- kmeans_iter_max: the same as the kmeans_iter_max argument. +- kmeans_nstart: the same as the kmeans_nstart argument. +- n_dim: contains numbers of the number of eigenvectors to be used in kmeans clustering. +- rand_seed: the same as the rand_seed argument. +- svm_train_inds: if SVM is used this item contains indexes of the training cells to be used for SC3 clustering and further SVM prediction. +- svm_study_inds: if SVM is used this item contains indexes of the cells to be predicted by SVM. +- n_cores: the same as the n_cores argument. + +@HELP@ + +@VERSION_HISTORY@ +]]></help> + <expand macro="citations" /> +</tool>