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annotate correlation_with_signature.xml @ 0:6f3da989b59d draft default tip

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author artbio
date Mon, 24 Jun 2019 07:18:35 -0400
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6f3da989b59d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_correlation commit 70c7abb20f76651e61325e3aa90809f6874f8b85
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1 <tool id="single_cell_gene_expression_correlations" name="single_cell_gene_expression_correlations" version="0.9.0">
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2 <description>between genes or with a signature of selected genes</description>
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3 <requirements>
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4 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
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5 <requirement type="package" version="4.0_3=r3.3.2_0">r-hmisc</requirement>
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6 </requirements>
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7 <stdio>
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8 <exit_code range="1:" level="fatal" description="Tool exception" />
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9 </stdio>
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10 <command detect_errors="exit_code"><![CDATA[
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11 Rscript $__tool_directory__/correlation_with_signature.R
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12 --expression_file '$expression_file'
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13 --signatures_file '$signatures_file'
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14 --sep
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15 #if $sep == 'tab':
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16 'tab'
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17 #elif $sep == 'comma':
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18 'comma'
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19 #end if
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20 --colnames '$colnames'
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21 --sig_corr '$sig_corr'
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22 --gene_corr '$gene_corr'
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23 --gene_corr_pval '$gene_corr_pval'
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24 ]]></command>
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25 <inputs>
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26 <param name="expression_file" type="data" format="txt" label="Expression data"
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27 help="a csv or tsv file that contains log2(CPM +1) expression values" />
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28 <param name="signatures_file" type="data" format="txt" label="signature values"
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29 help="a csv or tsv file that contains cell signatures" />
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30 <param name="sep" type="select" label="Indicate column separator"
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31 help="Note that all input files must have the same format">
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32 <option value="tab" selected="true">Tabs</option>
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33 <option value="comma">Comma</option>
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34 </param>
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35 <param name="colnames" type="select" label="Firt row contains column names"
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36 help="chose whether your files contain a header row (often a good idea)" >
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37 <option value="TRUE" selected="true">True</option>
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38 <option value="FALSE">False</option>
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39 </param>
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40 </inputs>
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41 <outputs>
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42 <data name="sig_corr" format="tabular" label="Genes-Signature correlations" />
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43 <data name="gene_corr" format="tabular" label="Correlations r (all)" />
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44 <data name="gene_corr_pval" format="tabular" label="Correlations p-values (all)" />
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="expression_file" value="gene_filtered_input.tsv" ftype="txt"/>
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49 <param name="signatures_file" value="signature.tsv" ftype="txt"/>
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50 <param name="sep" value='tab' />
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51 <param name="colnames" value="TRUE"/>
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52 <output name="sig_corr" file="sig_corr.tsv" ftype="tabular"/>
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53 <output name="gene_corr" file="gene_corr.tsv" ftype="tabular"/>
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54 <output name="gene_corr_pval" file="gene_corr_pval.tsv" ftype="tabular"/>
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55 </test>
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56 </tests>
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57 <help>
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58
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59 **What it does**
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60
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61 The tools computes a table of pairwise expression correlations between **selected genes**
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62 in single-cell RNAseq data, as well as a table of correlation between the expression of
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63 these selected genes and the value of a signature (must be a scalar for each library)
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64 across the single-cell data
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65
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66 **Inputs**
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67
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68 - a table of expression values (e.E. log10(CPM+1), etc...) of **selected genes** from single-cell RNAseq sequencing libraries (columns)
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69 These genes may be selected for their significant differential expression, because they
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70 belong to a specific pathway, etc.
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71 - a table of signature values for the single-cell RNAseq sequencing datasets
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72 The table should have 2 columns (Cell-identifier and signature-value). The signature
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73 values are scalars, one value per cell-identifier and are in the second column.
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74
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75 **Outputs**
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76
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77 - Correlation table between the signature score and selected gene expression. There is three columns:
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78 - gene name
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79 - Pearson_correlation : Pearson correlation value
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80 - p_value : associated p-value
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81 - Gene - Gene correlation table. It's a n x n matrix of correlation values where n is the number of selected genes.
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82 - Gene - Gene correlation associated p-values table. It has the same dimensions as Gene-Gene correlation table but for p-values.
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83
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84 </help>
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85 <citations>
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86 <citation type="bibtex">
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87 @Manual{,
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88 title = {R: A Language and Environment for Statistical Computing},
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89 author = {{R Core Team}},
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90 organization = {R Foundation for Statistical Computing},
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91 address = {Vienna, Austria},
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92 year = {2014},
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93 url = {http://www.R-project.org/},
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94 }
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95 </citation>
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96 </citations>
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97 </tool>