Mercurial > repos > ebi-gxa > sc3_prepare

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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 11:30:49 -0400
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9a2b61bfdaa9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id="sc3_prepare" name="SC3 Prepare" version="@TOOL_VERSION@+galaxy0">
9a2b61bfdaa9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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3 <description>a sc3 SingleCellExperiment object</description>
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4 <macros>
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5 <import>sc3-macros.xml</import>
9a2b61bfdaa9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
9a2b61bfdaa9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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9 sc3-sc3-prepare.R -i '${scater_log}' -o '${sc3_prepared}' -t 1
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10
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11 #if $gene_filter.use:
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12 -f TRUE
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13 -p '${gene_filter.pct_dropout_min}'
9a2b61bfdaa9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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14 -q '${gene_filter.pct_dropout_max}'
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15 #end if
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16 #if $d_region_min:
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17 -d '${d_region_min}'
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18 #end if
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19 #if $d_region_max:
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20 -d '${d_region_max}'
9a2b61bfdaa9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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21 #end if
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22 #if $svm_num_cells:
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23 -n '${svm_num_cells}'
9a2b61bfdaa9 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4
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24 #end if
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25 #if $svm_train_inds:
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26 -r '${svm_train_inds}'
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27 #end if
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28 #if $svm_max:
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29 -m '${svm_max}'
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30 #end if
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31 #if $seed:
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32 -s '${seed}'
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33 #end if
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34 #if $kmeans_nstart:
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35 -k '${kmeans_nstart}'
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36 #end if
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37 #if $kmeans_iter_max:
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38 -a '${kmeans_iter_max}'
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39 #end if
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40
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41 ]]></command>
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42
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43 <inputs>
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44 <param name="scater_log" type="data" format="rdata" label="Serialised SingleCellExperiment object normalised by scater"/>
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45
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46 <conditional name="gene_filter">
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47 <param name="use" argument="--gene-filter" type="boolean" label="Perform gene filtering?"
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48 help="A boolean variable which defines whether to perform gene filtering before SC3 clustering."/>
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49 <when value="true">
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50 <param name="pct_dropout_min" argument="--pct-dropout-min" type="integer" value="10" label="Minimum percent of dropouts"
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51 help="An integer value. Genes with percent of dropouts smaller than this value are filtered out before clustering."/>
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52 <param name="pct_dropout_max" argument="--pct-dropout-max" type="integer" value="90" label="Maximum percent of dropouts"
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53 help="An integer value. Genes with percent of dropouts larger than this value are filtered out before clustering."/>
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54 </when>
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55 <when value="false"/>
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56 </conditional>
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57
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58 <param name="d_region_min" argument="--d-region-min" type="float" value="0.04" optional="true"
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59 label="Minimum number of eigenvectors used for kmeans clustering as a fraction of the total number of cells"/>
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60
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61 <param name="d_region_max" argument="--d-region-max" type="float" value="0.07" optional="true"
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62 label="Maximum number of eigenvectors used for kmeans clustering as a fraction of the total number of cells"/>
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63
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64 <param name="svm_num_cells" argument="--svm-num-cells" type="integer" optional="true"
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65 label="Number of randomly selected training cells to be used for SVM prediction."/>
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66
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67 <param name="svm_train_inds" argument="--svm-train-inds" type="data" format="txt" optional="true"
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68 label="Text file with one integer per line defining indices of training cells that should be used for SVM training"/>
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69
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70 <param name="svm_max" argument="--svm-max" type="integer" value="5000"
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71 label="The number of cells below which SVM are not run"/>
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72
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73 <param name="seed" argument="--rand-seed" type="integer" value="1" optional="true" label="Seed of the random number generator"
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74 help="SC3 is a stochastic method, so setting the rand_seed to a fixed values can be used for reproducibility purposes."/>
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75
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76 <param name="kmeans_nstart" argument="--kmeans-nstart" type="integer" optional="true" label="Number of random starts for kmeans"
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77 help="When unspecified, default to 1000 for up to 2000 cells and 50 for more than 2000 cells."/>
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79 <param name="kmeans_iter_max" argument="--kmeans-iter-max" type="integer" optional="true" label="Maximum number of iterations for kmeans"
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80 help="When unspecified, default to 1e+9."/>
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81 </inputs>
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82
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83 <outputs>
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84 <data name="sc3_prepared" format="rdata" label="${tool.name} on ${on_string}: serialised sc3 SingleCellExperiment object"/>
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85 </outputs>
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86
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87 <tests>
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88 <test>
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89 <param name="scater_log" value="scater_log.rdata"/>
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90 <output name="sc3_prepared" file="sc3_prepared.rdata"/>
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91 </test>
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92 </tests>
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93
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94 <help><![CDATA[
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95
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96 ==================================================================================
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97 This function prepares an object of SingleCellExperiment class for SC3 clustering.
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98 ==================================================================================
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99 It creates and populates the following items of the sc3 slot of the metadata(object):
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100
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101 - kmeans_iter_max: the same as the kmeans_iter_max argument.
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102 - kmeans_nstart: the same as the kmeans_nstart argument.
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103 - n_dim: contains numbers of the number of eigenvectors to be used in kmeans clustering.
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104 - rand_seed: the same as the rand_seed argument.
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105 - 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.
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106 - svm_study_inds: if SVM is used this item contains indexes of the cells to be predicted by SVM.
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107 - n_cores: the same as the n_cores argument.
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108
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109 @HELP@
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110
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111 @VERSION_HISTORY@
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112 ]]></help>
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113 <expand macro="citations" />
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114 </tool>