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author artbio
date Tue, 09 Jul 2019 10:52:09 -0400
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1 <tool id="signature_score" name="Compute signature scores" version="0.9.1">
0
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2 <description>in single cell RNAseq</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="2.2.1=r3.3.2_0">r-ggplot2</requirement>
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6 <requirement type="package" version="2.3=r3.3.2_0">r-gridextra</requirement>
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7 <requirement type="package" version="1.6.9=r3.3.2_0">r-psych</requirement>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1:" level="fatal" description="Tool exception" />
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11 </stdio>
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12 <command detect_errors="exit_code"><![CDATA[
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13 Rscript $__tool_directory__/signature_score.R
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14 --input $input
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15 --sep
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16 #if $sep == 'tab':
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17 'tab'
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18 #elif $sep == 'comma':
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19 'comma'
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20 #end if
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21 --genes '$genes'
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22 --percentile_threshold '$threshold'
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23 --output '$output'
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24 --stats '$stats'
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25 --pdf '$pdf'
1
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26 --correlations '$correlations'
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27 --covariances '$covariances'
0
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28 ]]></command>
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29 <inputs>
1
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30 <param name="input" type="data" format="txt,tabular" label="Raw counts of expression data"/>
0
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31 <param name="sep" type="select" label="Indicate column separator">
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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="genes" type="text" value="" label="Comma-separated list of genes to include in signature"
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36 help="Comma-separated list of genes to include in signature, eg &quot;ZNF454,GAPDH,LAIR1,ACAD9,CHTOP&quot;" />
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37 <param name="threshold" type="float" value="20.0" label="Threshold to keep a proposed gene in the effective signature"
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38 help="signature gene that are not expressed in at least this percentage of cells will not be kept to compute the effective signature" />
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39 </inputs>
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40 <outputs>
1
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41 <data name="pdf" format="pdf" label="Signatures plots from ${on_string}" />
0
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42 <data name="output" format="tabular" label="signature scores from ${on_string}" />
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43 <data name="stats" format="tabular" label="genes statistics from ${on_string}" />
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44 <data name="correlations" format="tabular" label="Signature genes correlations" />
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45 <data name="covariances" format="tabular" label="Signature genes covariances" />
0
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46 </outputs>
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47 <tests>
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48 <test>
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49 <param name="input" value="gene_filtered_input.tsv" ftype="txt"/>
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50 <param name="sep" value='tab' />
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51 <param name="genes" value="ZNF454,GAPDH,LAIR1,ACAD9,CHTOP" />
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52 <output name="pdf" file="signature.pdf" ftype="pdf" compare="sim_size" delta="200" />
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53 <output name="output" file="signature.tsv" ftype="tabular"/>
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54 <output name="stats" file="gene_stats.tsv" ftype="tabular"/>
1
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55 <output name="correlations" file="correlations.tsv" ftype="tabular"/>
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56 <output name="covariances" file="covariances.tsv" ftype="tabular"/>
0
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57 </test>
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58 </tests>
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59 <help>
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60
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61 **What it does**
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62
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63 The tools takes a table of _normalized_ gene expression values (rows) in single cell RNAseq library sequencing (columns)
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64 and a comma-separated list of genes, and returns in a table the geometric mean of expression of these
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65 genes for each cell/library. This geometric mean is considered as the score for the genes signature for a given cell/library.
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66
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67
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68 **Inputs**
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69
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70 A table of comma (csv) or tabulation (tsv) separated values.
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71 Gene names should be in the first column and cell names should be in the first row.
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72 Note that in a number of a csv files, header of the gene column is omitted, resulting in
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73 a first row with one item less than in other rows. This is handled by the tool that
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74 recognises this situation.
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75
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76 A comma separated list of genes desired as contributing to the signature score of the cell/library
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77
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78 The expression threshold for signature genes (the aforementioned gene list) to be effectively
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79 taken into account to compute signature scores. By default, genes are taken into account if
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80 they are expressed in at least 20% of cells/libraries
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81
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82 ** Outputs **
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83 The tools returns a table "signature scores" that contains
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84
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85 * the cell/library identifier
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86 * the signature score for this identifier
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87 * the rate of the signature score, ie whether it is higher (HIGH) or lower (LOW) that the average signature score in all cells/libraries
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88 * the number of genes detected in the cell/library
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89 * the total number of aligned reads in the cell/library
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90
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91 </help>
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92 <citations>
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93 <citation type="bibtex">
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94 @Manual{,
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95 title = {R: A Language and Environment for Statistical Computing},
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96 author = {{R Core Team}},
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97 organization = {R Foundation for Statistical Computing},
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98 address = {Vienna, Austria},
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99 year = {2014},
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100 url = {http://www.R-project.org/},
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101 }
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102 </citation>
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103 </citations>
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104 </tool>