Mercurial > repos > artbio > gsc_gene_expression_correlations
annotate correlation_with_signature.xml @ 0:734ab9c5595a draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
author | artbio |
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date | Mon, 24 Jun 2019 13:38:39 -0400 |
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children | 8ad272e0b640 |
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734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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1 <tool id="single_cell_gene_expression_correlations" name="single-cell gene expression correlations" version="0.9.0"> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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2 <description>between genes or with a signature of selected genes</description> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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3 <requirements> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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4 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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5 <requirement type="package" version="4.0_3=r3.3.2_0">r-hmisc</requirement> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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6 </requirements> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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7 <stdio> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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8 <exit_code range="1:" level="fatal" description="Tool exception" /> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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9 </stdio> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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10 <command detect_errors="exit_code"><![CDATA[ |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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11 Rscript $__tool_directory__/correlation_with_signature.R |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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12 --expression_file '$expression_file' |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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13 --signatures_file '$signatures_file' |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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14 --sep |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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15 #if $sep == 'tab': |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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16 'tab' |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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17 #elif $sep == 'comma': |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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18 'comma' |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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19 #end if |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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20 --colnames '$colnames' |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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21 --sig_corr '$sig_corr' |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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22 --gene_corr '$gene_corr' |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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23 --gene_corr_pval '$gene_corr_pval' |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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24 ]]></command> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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25 <inputs> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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26 <param name="expression_file" type="data" format="txt,tabular" label="Expression data" |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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27 help="a csv or tsv file that contains log2(CPM +1) expression values" /> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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28 <param name="signatures_file" type="data" format="txt,tabular" label="signature values" |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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29 help="a csv or tsv file that contains cell signatures" /> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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30 <param name="sep" type="select" label="Indicate column separator" |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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31 help="Note that all input files must have the same format"> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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32 <option value="tab" selected="true">Tabs</option> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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33 <option value="comma">Comma</option> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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34 </param> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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35 <param name="colnames" type="select" label="Firt row contains column names" |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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36 help="chose whether your files contain a header row (often a good idea)" > |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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37 <option value="TRUE" selected="true">True</option> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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38 <option value="FALSE">False</option> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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39 </param> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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40 </inputs> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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41 <outputs> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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42 <data name="sig_corr" format="tabular" label="Genes-Signature correlations" /> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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43 <data name="gene_corr" format="tabular" label="Correlations r (all)" /> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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44 <data name="gene_corr_pval" format="tabular" label="Correlations p-values (all)" /> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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45 </outputs> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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46 <tests> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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47 <test> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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48 <param name="expression_file" value="gene_filtered_input.tsv" ftype="txt"/> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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49 <param name="signatures_file" value="signature.tsv" ftype="txt"/> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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50 <param name="sep" value='tab' /> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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51 <param name="colnames" value="TRUE"/> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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52 <output name="sig_corr" file="sig_corr.tsv" ftype="tabular"/> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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53 <output name="gene_corr" file="gene_corr.tsv" ftype="tabular"/> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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54 <output name="gene_corr_pval" file="gene_corr_pval.tsv" ftype="tabular"/> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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55 </test> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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56 </tests> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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57 <help> |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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58 |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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59 **What it does** |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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60 |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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61 The tools computes a table of pairwise expression correlations between **selected genes** |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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62 in single-cell RNAseq data, as well as a table of correlation between the expression of |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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63 these selected genes and the value of a signature (must be a scalar for each library) |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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64 across the single-cell data |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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65 |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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66 **Inputs** |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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67 |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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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) |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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69 These genes may be selected for their significant differential expression, because they |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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70 belong to a specific pathway, etc. |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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71 - a table of signature values for the single-cell RNAseq sequencing datasets |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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72 The table should have 2 columns (Cell-identifier and signature-value). The signature |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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73 values are scalars, one value per cell-identifier and are in the second column. |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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74 |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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75 **Outputs** |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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76 |
734ab9c5595a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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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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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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80 - p_value : associated p-value |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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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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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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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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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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83 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_gene_expression_correlations commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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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> |