Mercurial > repos > artbio > gsc_signature_score
annotate signature_score.xml @ 1:01b2c4fcada8 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 06c8d40814f68cbf4d24b2ea70a11407bc40d072
author | artbio |
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date | Mon, 24 Jun 2019 19:17:53 -0400 |
parents | baf7a079bce0 |
children | e08419b8ec24 |
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baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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1 <tool id="signature_score" name="Compute signature scores" version="0.9.0"> |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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2 <description>in single cell RNAseq</description> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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3 <requirements> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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4 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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5 <requirement type="package" version="2.2.1=r3.3.2_0">r-ggplot2</requirement> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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6 <requirement type="package" version="2.3=r3.3.2_0">r-gridextra</requirement> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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7 <requirement type="package" version="1.6.9=r3.3.2_0">r-psych</requirement> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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8 </requirements> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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9 <stdio> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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10 <exit_code range="1:" level="fatal" description="Tool exception" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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11 </stdio> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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12 <command detect_errors="exit_code"><![CDATA[ |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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13 Rscript $__tool_directory__/signature_score.R |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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14 --input $input |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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15 --sep |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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16 #if $sep == 'tab': |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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17 'tab' |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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18 #elif $sep == 'comma': |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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19 'comma' |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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20 #end if |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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21 --genes '$genes' |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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22 --percentile_threshold '$threshold' |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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23 --output '$output' |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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24 --stats '$stats' |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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25 --pdf '$pdf' |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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26 ]]></command> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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27 <inputs> |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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28 <param name="input" type="data" format="txt,tabular" label="Raw counts of expression data"/> |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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29 <param name="sep" type="select" label="Indicate column separator"> |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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30 <option value="tab" selected="true">Tabs</option> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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31 <option value="comma">Comma</option> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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32 </param> |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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33 <param name="genes" type="text" value="" label="Comma-separated list of genes to include in signature" |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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34 help="Comma-separated list of genes to include in signature, eg "ZNF454,GAPDH,LAIR1,ACAD9,CHTOP"" /> |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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35 <param name="threshold" type="float" value="20.0" label="Threshold to keep a proposed gene in the effective signature" |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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36 help="signature gene that are not expressed in at least this percentage of cells will not be kept to compute the effective signature" /> |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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37 </inputs> |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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38 <outputs> |
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01b2c4fcada8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 06c8d40814f68cbf4d24b2ea70a11407bc40d072
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39 <data name="pdf" format="pdf" label="Signatures plots from ${on_string}" /> |
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baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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40 <data name="output" format="tabular" label="signature scores from ${on_string}" /> |
1
01b2c4fcada8
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 06c8d40814f68cbf4d24b2ea70a11407bc40d072
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41 <data name="stats" format="tabular" label="genes statistics from ${on_string}" /> |
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baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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42 </outputs> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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43 <tests> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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44 <test> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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45 <param name="input" value="gene_filtered_input.tsv" ftype="txt"/> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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46 <param name="sep" value='tab' /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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47 <param name="genes" value="ZNF454,GAPDH,LAIR1,ACAD9,CHTOP" /> |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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48 <output name="pdf" file="signature.pdf" ftype="pdf" compare="sim_size" delta="200" /> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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49 <output name="output" file="signature.tsv" ftype="tabular"/> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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50 <output name="stats" file="gene_stats.tsv" ftype="tabular"/> |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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51 </test> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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52 </tests> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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53 <help> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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54 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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55 **What it does** |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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56 |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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57 The tools takes a table of _normalized_ gene expression values (rows) in single cell RNAseq library sequencing (columns) |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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58 and a comma-separated list of genes, and returns in a table the geometric mean of expression of these |
baf7a079bce0
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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59 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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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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60 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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61 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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62 **Inputs** |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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63 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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64 A table of comma (csv) or tabulation (tsv) separated values. |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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65 Gene names should be in the first column and cell names should be in the first row. |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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66 Note that in a number of a csv files, header of the gene column is omitted, resulting in |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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67 a first row with one item less than in other rows. This is handled by the tool that |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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68 recognises this situation. |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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69 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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70 A comma separated list of genes desired as contributing to the signature score of the cell/library |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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71 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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72 The expression threshold for signature genes (the aforementioned gene list) to be effectively |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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73 taken into account to compute signature scores. By default, genes are taken into account if |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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74 they are expressed in at least 20% of cells/libraries |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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75 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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76 ** Outputs ** |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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77 The tools returns a table "signature scores" that contains |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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78 |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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79 * the cell/library identifier |
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80 * the signature score for this identifier |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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81 * 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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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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82 * the number of genes detected in the cell/library |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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83 * the total number of aligned reads in the cell/library |
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84 |
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85 </help> |
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86 <citations> |
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87 <citation type="bibtex"> |
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88 @Manual{, |
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89 title = {R: A Language and Environment for Statistical Computing}, |
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90 author = {{R Core Team}}, |
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91 organization = {R Foundation for Statistical Computing}, |
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92 address = {Vienna, Austria}, |
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93 year = {2014}, |
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94 url = {http://www.R-project.org/}, |
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95 } |
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96 </citation> |
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97 </citations> |
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98 </tool> |