annotate correlation_with_signature.xml @ 2:b49295546f29 draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 91d59a3a90a9bdb64ec70000b69a864285411d9a

<tool id="single_cell_gene_expression_correlations" name="single-cell gene expression correlations" version="4.3.1+galaxy0" profile="21.01">
    <description>between genes or with a signature of selected genes</description>
    <requirements>
        <requirement type="package" version="1.7.3">r-optparse</requirement>
        <requirement type="package" version="5.1_1">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>