Mercurial > repos > artbio > gsc_gene_expression_correlations
view correlation_with_signature.xml @ 1:8ad272e0b640 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
author | artbio |
---|---|
date | Mon, 02 Sep 2019 04:38:59 -0400 |
parents | 734ab9c5595a |
children | b49295546f29 |
line wrap: on
line source
<tool id="single_cell_gene_expression_correlations" name="single-cell gene expression correlations" version="0.9.1"> <description>between genes or with a signature of selected genes</description> <requirements> <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement> <requirement type="package" version="4.0_3=r3.3.2_0">r-hmisc</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> </stdio> <command detect_errors="exit_code"><![CDATA[ Rscript $__tool_directory__/correlation_with_signature.R --expression_file '$expression_file' --signatures_file '$signatures_file' --sep #if $sep == 'tab': 'tab' #elif $sep == 'comma': 'comma' #end if --colnames '$colnames' --sig_corr '$sig_corr' --gene_corr '$gene_corr' --gene_corr_pval '$gene_corr_pval' ]]></command> <inputs> <param name="expression_file" type="data" format="txt,tabular" label="Expression data" help="a csv or tsv file that contains log2(CPM +1) expression values" /> <param name="signatures_file" type="data" format="txt,tabular" label="signature values" help="a csv or tsv file that contains cell signatures" /> <param name="sep" type="select" label="Indicate column separator" help="Note that all input files must have the same format"> <option value="tab" selected="true">Tabs</option> <option value="comma">Comma</option> </param> <param name="colnames" type="select" label="Firt row contains column names" help="chose whether your files contain a header row (often a good idea)" > <option value="TRUE" selected="true">True</option> <option value="FALSE">False</option> </param> </inputs> <outputs> <data name="sig_corr" format="tabular" label="Genes-Signature correlations" /> <data name="gene_corr" format="tabular" label="Correlations r (all)" /> <data name="gene_corr_pval" format="tabular" label="Correlations p-values (all)" /> </outputs> <tests> <test> <param name="expression_file" value="gene_filtered_input.tsv" ftype="txt"/> <param name="signatures_file" value="signature.tsv" ftype="txt"/> <param name="sep" value='tab' /> <param name="colnames" value="TRUE"/> <output name="sig_corr" file="sig_corr.tsv" ftype="tabular"/> <output name="gene_corr" file="gene_corr.tsv" ftype="tabular"/> <output name="gene_corr_pval" file="gene_corr_pval.tsv" ftype="tabular"/> </test> </tests> <help> **What it does** The tools computes a table of pairwise expression correlations between **selected genes** in single-cell RNAseq data, as well as a table of correlation between the expression of these selected genes and the value of a signature (must be a scalar for each library) across the single-cell data **Inputs** - a table of expression values (e.E. log10(CPM+1), etc...) of **selected genes** from single-cell RNAseq sequencing libraries (columns) These genes may be selected for their significant differential expression, because they belong to a specific pathway, etc. - a table of signature values for the single-cell RNAseq sequencing datasets The table should have 2 columns (Cell-identifier and signature-value). The signature values are scalars, one value per cell-identifier and are in the second column. **Outputs** - Correlation table between the signature score and selected gene expression. There is three columns: - gene name - Pearson_correlation : Pearson correlation value - p_value : associated p-value - Gene - Gene correlation table. It's a n x n matrix of correlation values where n is the number of selected genes. - Gene - Gene correlation associated p-values table. It has the same dimensions as Gene-Gene correlation table but for p-values. </help> <citations> <citation type="bibtex"> @Manual{, title = {R: A Language and Environment for Statistical Computing}, author = {{R Core Team}}, organization = {R Foundation for Statistical Computing}, address = {Vienna, Austria}, year = {2014}, url = {http://www.R-project.org/}, } </citation> </citations> </tool>