Mercurial > repos > artbio > gsc_high_dimensions_visualisation
annotate high_dim_visu.xml @ 4:8e17c31c536a draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
| author | artbio |
|---|---|
| date | Thu, 11 Jul 2019 12:31:28 -0400 |
| parents | 8e44c9e18a56 |
| children | 569334568afa |
| rev | line source |
|---|---|
|
4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
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1 <tool id="high_dimensions_visualisation" name="Generate PCA, tSNE and HCPC" version="0.9.4"> |
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0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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2 <description>from highly dimensional expression data</description> |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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3 <requirements> |
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4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
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diff
changeset
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4 <requirement type="package" version="1.6.2=r35h6115d3f_0">r-optparse</requirement> |
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8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
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5 <requirement type="package" version="1.42=r35h6115d3f_0">r-factominer</requirement> |
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8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
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6 <requirement type="package" version="1.0.5">r-factoextra</requirement> |
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8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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changeset
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7 <requirement type="package" version="0.15=r351he1b5a44_0">r-rtsne</requirement> |
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8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff
changeset
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8 <requirement type="package" version="0.4.7=r351h6115d3f_0">r-ggfortify</requirement> |
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8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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9 <requirement type="package" version="1.1.9=r351h0357c0b_0">r-clusterr</requirement> |
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0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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10 </requirements> |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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11 <stdio> |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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12 <exit_code range="1:" level="fatal" description="Tool exception" /> |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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13 </stdio> |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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14 <command detect_errors="exit_code"><![CDATA[ |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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15 Rscript $__tool_directory__/high_dim_visu.R |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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changeset
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16 --data '$input' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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17 --sep '$input_sep' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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18 --colnames '$input_header' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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19 #if $factor_condition.factor_choice == 'Yes' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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20 --factor '$factor_condition.factor' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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21 #end if |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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22 #if $labels == "yes": |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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23 --labels 'TRUE' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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24 #else |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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25 --labels 'FALSE' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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26 #end if |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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27 #if $coord == "yes": |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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28 --table_coordinates '$table_coordinates' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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29 #end if |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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30 --visu_choice '$visualisation.visu_choice' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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31 #if $visualisation.visu_choice == "tSNE": |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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32 --Rtsne_seed '$visualisation.Rtsne_seed' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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33 --Rtsne_perplexity '$visualisation.Rtsne_perplexity' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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34 --Rtsne_theta '$visualisation.Rtsne_theta' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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35 --Rtsne_max_iter '$visualisation.Rtsne_max_iter' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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36 --Rtsne_dims '$visualisation.Rtsne_dims' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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37 --Rtsne_initial_dims '$visualisation.Rtsne_initial_dims' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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38 --Rtsne_pca '$visualisation.Rtsne_pca' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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39 --Rtsne_pca_center '$visualisation.Rtsne_pca_center' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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40 --Rtsne_pca_scale '$visualisation.Rtsne_pca_scale' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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41 --Rtsne_normalize '$visualisation.Rtsne_normalize' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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42 --Rtsne_exaggeration_factor '$visualisation.Rtsne_exaggeration_factor' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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43 #end if |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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44 |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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45 #if $visualisation.visu_choice == "HCPC": |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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46 --HCPC_ncluster '$visualisation.HCPC_ncluster' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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47 --HCPC_npc '$visualisation.HCPC_npc' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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48 --HCPC_metric '$visualisation.HCPC_metric' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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49 --HCPC_method '$visualisation.HCPC_method' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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50 --HCPC_consol '$visualisation.HCPC_consol' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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51 --HCPC_itermax '$visualisation.HCPC_itermax' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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52 --HCPC_min '$visualisation.HCPC_min' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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53 --HCPC_max '$visualisation.HCPC_max' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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54 --HCPC_clusterCA '$visualisation.HCPC_clusterCA' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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55 --HCPC_kk '$visualisation.HCPC_kk' |
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4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
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56 #if $visualisation.res_clustering == "yes": |
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8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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57 --HCPC_clust '$HCPC_clust' |
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8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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58 #end if |
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0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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59 #end if |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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60 |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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61 #if $visualisation.visu_choice == "PCA": |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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62 --PCA_npc '$visualisation.PCA_npc' |
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4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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63 --PCA_x_axis '$visualisation.PCA_x_axis' |
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8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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64 --PCA_y_axis '$visualisation.PCA_y_axis' |
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0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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65 #end if |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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66 |
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4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
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67 #if $visualisation.visu_choice == "HCPC" and $factor_condition.factor_choice == "Yes": |
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8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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68 --mutual_info '$mutual_info' |
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8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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69 #end if |
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8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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70 |
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0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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71 --pdf_out '$pdf_out' |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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72 |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
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73 ]]></command> |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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74 <inputs> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
75 <param name="input" type="data" format="txt,tabular" label="expression data"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
76 <param name="input_sep" type="select" label="Input column separator"> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
77 <option value="tab" selected="true">Tabs</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
78 <option value=",">Comma</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
79 </param> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
80 <param name="input_header" type="select" label="Consider first line of input file as header?"> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
81 <option value="TRUE" selected="true">Yes</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
82 <option value="FALSE">No</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
83 </param> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
84 <param name="labels" type="select" label="Add sample labels to scatter plot" > |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
85 <option value="no" selected="true">No Labels</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
86 <option value="yes" >Label points</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
87 </param> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
88 <conditional name="factor_condition"> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
89 <param label="Do you wish to contrast cells with a factor" name="factor_choice" type="select"> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
90 <option value="Yes">Yes</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
91 <option value="No" selected="true">No</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
92 </param> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
93 <when value="Yes"> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
94 <param name="factor" type="data" format="tabular" label="Factor to constrast data" |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
95 help="A two-column data frame, first column contains data labels, second column contains the levels of a factor to contrast visualisation" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
96 </when> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
97 <when value="No"> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
98 </when> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
99 </conditional> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
100 <conditional name="visualisation"> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
101 <param label="Choose visualisation method" name="visu_choice" type="select"> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
102 <option value="PCA" selected="True">PCA</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
103 <option value="HCPC">HCPC</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
104 <option value="tSNE">t-SNE</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
105 </param> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
106 <when value="tSNE"> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
107 <param name="Rtsne_seed" value="42" type="integer" label="Seed value for reproducibility of t-SNE" help="Set to 42 as default" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
108 <param name="Rtsne_dims" value="2" type="integer" label="dims (t-SNE)" help="Output dimensionality (should not be greater than 3)" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
109 <param name="Rtsne_pca" type="select" label="pca (t-SNE)" help="Whether an initial PCA step should be performed" > |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
110 <option value="TRUE" selected="true">Yes</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
111 <option value="FALSE">False</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
112 </param> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
113 <param name="Rtsne_initial_dims" value="50" type="integer" label="initial dims (t-SNE)" help="The number of dimensions that should be retained in the initial PCA step" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
114 <param name="Rtsne_pca_center" type="select" label="Centering data" help="Should data be centered before pca is applied? " > |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
115 <option value="TRUE" selected="true">Yes</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
116 <option value="FALSE">False</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
117 </param> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
118 <param name="Rtsne_pca_scale" type="select" label="Scalling data" help="Should data be scaled before pca is applied? " > |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
119 <option value="TRUE">Yes</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
120 <option value="FALSE" selected="true">False</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
121 </param> |
|
4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
122 <param name="Rtsne_normalize" type="select" label="Normalisation of data" |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
123 help="Should variables (gene expressions) be normalized internally prior to distance calculations? " > |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
124 <option value="TRUE" selected="true">Yes</option> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
125 <option value="FALSE">False</option> |
|
0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
126 </param> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
127 <param name="Rtsne_perplexity" value="10.0" type="float" label="perplexity (t-SNE)" help="should be less than ((nbr observations)-1)/3" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
128 <param name="Rtsne_theta" value="1.0" type="float" label="theta (t-SNE)"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
129 <param name="Rtsne_exaggeration_factor" value="12.0" type="float" label="Exageration factor" help="Exaggeration factor used to multiply the P matrix in the first part of the optimization" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
130 <param name="Rtsne_max_iter" value="1000" type="integer" label="Number of iterations (default: 1000)" |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
131 help="The number of iterations that Rtsne executes to improve low dim representation (gradient descent optimization)" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
132 </when> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
133 <when value="HCPC"> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
134 <param name="HCPC_npc" value="5" type="integer" label="Number of principal components to keep" |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
135 help="The number of dimensions which are kept for HCPC analysis (default=5)" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
136 <param name="HCPC_ncluster" value="-1" type="integer" label="Number of clusters in Hierar. Clustering" |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
137 help="nb.clust, the number of clusters to consider in the hierarchical clustering. (default : -1, let HCPC to optimize the number)" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
138 <param name="HCPC_metric" type="select" label="Dissimilarity metric" help="Metric to be used for calculating dissimilarities between observations, available 'euclidian' or 'manhattan'? " > |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
139 <option value="euclidian" selected="true">euclidian</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
140 <option value="manhattan">manhattan</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
141 </param> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
142 <param name="HCPC_method" type="select" label="Clustering method" help="Clustering method between 'ward', 'average', 'single', 'complete', 'weighted' " > |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
143 <option value="ward" selected="true">ward</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
144 <option value="average">average</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
145 <option value="single">single</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
146 <option value="complete">complete</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
147 <option value="weighted">weighted</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
148 </param> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
149 <param name="HCPC_consol" type="select" label="k-means consolidation" help="If TRUE, a k-means consolidation is performed" > |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
150 <option value="TRUE" selected="true">Yes</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
151 <option value="FALSE">False</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
152 </param> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
153 <param name="HCPC_itermax" value="10" type="integer" label="Maximum number of iterations for consolidation" |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
154 help=" (default=10)" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
155 <param name="HCPC_min" value="3" type="integer" label="min number of clusters" |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
156 help=" The least possible number of clusters suggested (default=3)" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
157 <param name="HCPC_max" value="-1" type="text" label="max number of clusters" |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
158 help=" The higher possible number of clusters suggested, by default the minimum between 10 and the number of individuals divided by 2. (default=-1)" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
159 <param name="HCPC_clusterCA" type="select" label="clusterCA, Clustering against rows or columns" help="default(rows)" > |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
160 <option value="rows" selected="true">Rows</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
161 <option value="cols">Columns</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
162 </param> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
163 <param name="HCPC_kk" value="-1" type="text" label="kk, Number of clusters used in a Kmeans preprocessing " |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
164 help="No k-means consolidation is done if a kk value is provided (default=-1)" /> |
|
4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
165 <param label="Return HCPC clustering table" name="res_clustering" type="select"> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
166 <option value="no" selected="True">No</option> |
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8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
167 <option value="yes">Yes</option> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
168 </param> |
|
0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
169 </when> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
170 <when value="PCA"> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
171 <param name="PCA_npc" value="5" type="integer" label="Number of principal components to keep" help="The number of dimensions which are kept for PCA analysis (default=5)" /> |
|
4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
172 <param name="PCA_x_axis" value="1" type="integer" label="First principal component to plot" help="X axis for PCA plot (default=1)" /> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
173 <param name="PCA_y_axis" value="2" type="integer" label="Second principal component to plot" help="Y axis for PCA plot (default=2)" /> |
|
0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
174 </when> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
175 </conditional> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
176 <param label="Return scatter plot table coordinates" name="coord" type="select"> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
177 <option value="no" selected="True">No</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
178 <option value="yes">Yes</option> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
179 </param> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
180 |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
181 </inputs> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
182 <outputs> |
|
1
c756ab726a85
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 06c8d40814f68cbf4d24b2ea70a11407bc40d072
artbio
parents:
0
diff
changeset
|
183 <data name="pdf_out" format="pdf" label="${visualisation.visu_choice} of ${on_string}" /> |
|
c756ab726a85
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 06c8d40814f68cbf4d24b2ea70a11407bc40d072
artbio
parents:
0
diff
changeset
|
184 <data name="table_coordinates" format="tabular" label="Scatter plot coordinates from ${visualisation.visu_choice} of ${on_string}" > |
|
0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
185 <filter>coord == 'yes'</filter> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
186 </data> |
|
4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
187 <data name="mutual_info" format="txt" label="External validation of clustering from ${visualisation.visu_choice} of ${on_string}" > |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
188 <filter>visualisation['visu_choice'] == 'HCPC' and factor_condition['factor_choice'] == 'Yes'</filter> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
189 </data> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
190 <data name="HCPC_clust" format="tabular" label="Clustering table from ${visualisation.visu_choice} of ${on_string}" > |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
191 <filter>visualisation['visu_choice'] == 'HCPC' and visualisation['res_clustering'] == 'yes'</filter> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
192 </data> |
|
0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
193 </outputs> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
194 <tests> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
195 <!-- test PCA --> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
196 <test> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
197 <param name="input" value="cpm_input.tsv" ftype="txt"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
198 <param name="labels" value="yes" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
199 <param name="visu_choice" value="PCA" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
200 <param name="factor_choice" value="No" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
201 <output name="pdf_out" file="pca.labels.pdf" ftype="pdf"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
202 </test> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
203 <test> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
204 <param name="input" value="cpm_input.tsv" ftype="txt"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
205 <param name="labels" value="no" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
206 <param name="visu_choice" value="PCA" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
207 <param name="factor_choice" value="No" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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208 <output name="pdf_out" file="pca.nolabels.pdf" ftype="pdf"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
209 </test> |
|
4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
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210 <!-- test PCA PC2 vs PC3 --> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
211 <test> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
212 <param name="input" value="cpm_input.tsv" ftype="txt"/> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
213 <param name="labels" value="no" /> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
214 <param name="visu_choice" value="PCA" /> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
215 <param name="factor_choice" value="No" /> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
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|
216 <param name="PCA_x_axis" value="2" /> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
217 <param name="PCA_y_axis" value="3" /> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
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218 <output name="pdf_out" file="pca.2vs3.pdf" ftype="pdf"/> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
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diff
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219 </test> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
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diff
changeset
|
220 |
|
0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
221 <!-- test Coordinates tables on PCA --> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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222 <test> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
223 <param name="input" value="cpm_input.tsv" ftype="txt"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
224 <param name="labels" value="no" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
225 <param name="visu_choice" value="PCA" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
226 <param name="coord" value="yes" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
227 <param name="factor_choice" value="No" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
228 <output name="pdf_out" file="pca.nolabels.pdf" ftype="pdf"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
229 <output name="table_coordinates" file="pca.coord.tab" ftype="tabular"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
230 </test> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
231 <!-- test factor contrasting on PCA --> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
232 <test> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
233 <param name="input" value="cpm_input.tsv" ftype="txt"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
234 <param name="labels" value="no" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
235 <param name="visu_choice" value="PCA" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
236 <param name="factor_choice" value="Yes" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
237 <param name="factor" value="factor.tsv" ftype="txt"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
238 <output name="pdf_out" file="pca.nolabels.factors.pdf" ftype="pdf"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
239 </test> |
|
2
7e7a2a4cfce2
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit e15ae06208ef1d3d42c0576ed28eb6ba10a36671
artbio
parents:
1
diff
changeset
|
240 <!-- test two-level factor contrasting on PCA --> |
|
7e7a2a4cfce2
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit e15ae06208ef1d3d42c0576ed28eb6ba10a36671
artbio
parents:
1
diff
changeset
|
241 <test> |
|
7e7a2a4cfce2
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit e15ae06208ef1d3d42c0576ed28eb6ba10a36671
artbio
parents:
1
diff
changeset
|
242 <param name="input" value="cpm_input.tsv" ftype="txt"/> |
|
7e7a2a4cfce2
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit e15ae06208ef1d3d42c0576ed28eb6ba10a36671
artbio
parents:
1
diff
changeset
|
243 <param name="labels" value="no" /> |
|
7e7a2a4cfce2
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit e15ae06208ef1d3d42c0576ed28eb6ba10a36671
artbio
parents:
1
diff
changeset
|
244 <param name="visu_choice" value="PCA" /> |
|
7e7a2a4cfce2
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit e15ae06208ef1d3d42c0576ed28eb6ba10a36671
artbio
parents:
1
diff
changeset
|
245 <param name="factor_choice" value="Yes" /> |
|
7e7a2a4cfce2
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit e15ae06208ef1d3d42c0576ed28eb6ba10a36671
artbio
parents:
1
diff
changeset
|
246 <param name="factor" value="2-lev_factor.tsv" ftype="txt"/> |
|
4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
247 <output name="pdf_out" file="pca.nolabels.2-lev-factor.pdf" compare="sim_size" ftype="pdf"/> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
248 </test> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
249 <!-- test numerical factor contrasting on PCA --> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
250 <test> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
251 <param name="input" value="cpm_input.tsv" ftype="txt"/> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
252 <param name="labels" value="no" /> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
253 <param name="visu_choice" value="PCA" /> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
254 <param name="factor_choice" value="Yes" /> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
255 <param name="factor" value="numeric_factor.tsv" ftype="txt"/> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
256 <output name="pdf_out" file="pca.nolabels.numerical-factor.pdf" compare="sim_size" ftype="pdf"/> |
|
2
7e7a2a4cfce2
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit e15ae06208ef1d3d42c0576ed28eb6ba10a36671
artbio
parents:
1
diff
changeset
|
257 </test> |
|
0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
258 <test> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
259 <param name="input" value="cpm_input.tsv" ftype="txt"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
260 <param name="labels" value="no" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
261 <param name="visu_choice" value="PCA" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
262 <param name="factor_choice" value="Yes" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
263 <param name="factor" value="shuffled_factor.tsv" ftype="txt"/> |
|
4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
264 <output name="pdf_out" file="pca.nolabels.factors.pdf" compare="sim_size" ftype="pdf"/> |
|
0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
265 </test> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
266 <!-- test HCPC --> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
267 <test> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
268 <param name="input" value="cpm_input.tsv" ftype="txt"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
269 <param name="labels" value="yes" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
270 <param name="visu_choice" value="HCPC" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
271 <param name="HCPC_npc" value="5"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
272 <param name="HCPC_ncluster" value="-1"/> |
|
4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
273 <output name="pdf_out" file="hcpc.labels.pdf" compare="sim_size" ftype="pdf"/> |
|
0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
274 </test> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
275 <!-- test factor contrasting on HCPC --> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
276 <test> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
277 <param name="input" value="cpm_input.tsv" ftype="txt"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
278 <param name="labels" value="no" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
279 <param name="visu_choice" value="HCPC" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
280 <param name="HCPC_npc" value="5"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
281 <param name="HCPC_ncluster" value="-1"/> |
|
4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
282 <param name="res_clustering" value="yes"/> |
|
0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
283 <param name="factor_choice" value="Yes" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
284 <param name="factor" value="factor.tsv" ftype="txt"/> |
|
4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
285 <output name="pdf_out" file="hcpc.nolabels.factor.pdf" compare="sim_size" ftype="pdf"/> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
286 <output name="mutual_info" file="hcpc.factor.extval.txt" ftype="txt"/> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
287 <output name="HCPC_clust" file="hcpc.clusters.tab" ftype="tabular"/> |
|
0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
288 </test> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
289 <test> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
290 <param name="input" value="cpm_input.tsv" ftype="txt"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
291 <param name="labels" value="no" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
292 <param name="HCPC_npc" value="5"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
293 <param name="HCPC_ncluster" value="-1"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
294 <param name="visu_choice" value="HCPC" /> |
|
4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
295 <output name="pdf_out" file="hcpc.nolabels.pdf" compare="sim_size" ftype="pdf"/> |
|
0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
296 </test> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
297 <test> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
298 <param name="input" value="cpm_input.tsv" ftype="txt"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
299 <param name="labels" value="yes" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
300 <param name="visu_choice" value="HCPC" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
301 <param name="coord" value="yes" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
302 <param name="HCPC_method" value="average"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
303 <param name="HCPC_metric" value="manhattan"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
304 <param name="HCPC_npc" value="4" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
305 <output name="pdf_out" file="hcpc-2.labels.pdf" ftype="pdf"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
306 <output name="table_coordinates" file="hcpc-2.coord.tab" ftype="tabular"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
307 </test> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
308 <test> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
309 <param name="input" value="cpm_input.tsv" ftype="txt"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
310 <param name="labels" value="yes" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
311 <param name="visu_choice" value="HCPC" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
312 <param name="coord" value="yes" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
313 <param name="HCPC_method" value="single"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
314 <param name="HCPC_metric" value="euclidian"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
315 <param name="HCPC_npc" value="4" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
316 <param name="HCPC_clusterCA" value="cols" /> |
|
4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
317 <output name="pdf_out" file="hcpc-3.labels.pdf" compare="sim_size" ftype="pdf"/> |
|
0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
318 <output name="table_coordinates" file="hcpc-3.coord.tab" ftype="tabular"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
319 </test> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
320 <!-- test t-SNE --> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
321 <test> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
322 <param name="input" value="cpm_input.tsv" ftype="txt"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
323 <param name="labels" value="yes" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
324 <param name="visu_choice" value="tSNE" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
325 <param name="Rtsne_seed" value="49"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
326 <param name="Rtsne_perplexity" value="10"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
327 <param name="Rtsne_theta" value="1" /> |
|
4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
328 <output name="pdf_out" file="tsne.labels.pdf" ftype="pdf" compare="sim_size" delta="500"/> |
|
0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
329 </test> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
330 <test> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
331 <param name="input" value="cpm_input.tsv" ftype="txt"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
332 <param name="labels" value="no" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
333 <param name="visu_choice" value="tSNE" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
334 <param name="Rtsne_seed" value="49"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
335 <param name="Rtsne_perplexity" value="10"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
336 <param name="Rtsne_theta" value="1" /> |
|
4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
337 <output name="pdf_out" file="tsne.nolabels.pdf" ftype="pdf" compare="sim_size" delta="500"/> |
|
0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
338 </test> |
|
4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
339 <!-- test factor contrasting on t-SNE --> |
|
0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
340 <test> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
341 <param name="input" value="cpm_input.tsv" ftype="txt"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
342 <param name="labels" value="yes" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
343 <param name="visu_choice" value="tSNE" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
344 <param name="factor_choice" value="Yes" /> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
345 <param name="factor" value="shuffled_factor.tsv" ftype="txt"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
346 <param name="Rtsne_seed" value="49"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
347 <param name="Rtsne_perplexity" value="10"/> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
348 <param name="Rtsne_theta" value="1" /> |
|
4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
349 <output name="pdf_out" file="tsne.labels.factor.pdf" ftype="pdf" compare="sim_size" delta="500"/> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
350 </test> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
351 <test> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
352 <param name="input" value="cpm_input.tsv" ftype="txt"/> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
353 <param name="labels" value="no" /> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
354 <param name="visu_choice" value="tSNE" /> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
355 <param name="Rtsne_seed" value="49" /> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
356 <param name="coord" value="yes" /> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
357 <param name="Rtsne_dims" value="3" /> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
358 <param name="Rtsne_perplexity" value="10"/> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
359 <param name="Rtsne_theta" value="1" /> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
360 <param name="Rtsne_normalize" value="FALSE" /> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
361 <output name="pdf_out" file="tsne-2.nolabels.pdf" ftype="pdf" compare="sim_size" delta="500"/> |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
362 <output name="table_coordinates" file="tsne-2.coord.tab" ftype="tabular" compare="sim_size" delta="500"/> |
|
0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
363 </test> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
364 </tests> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
365 <help> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
366 |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
367 **What it does** |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
368 |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
369 Takes as an input a matrix of n observations (columns, generally n RNAseq library) of k variables |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
370 (rows, generally k genes). |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
371 |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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372 k variables define a space of k dimensions. Any observation |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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373 of k expression values for k genes (the purpose of one RNAseq experiment) can be assigned |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
374 to a position in the k-dim space, of coordinates c1, c2, c3, ..., ck. |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
375 |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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376 Since visualisation in more than 3 dimensions is not easy for a human beeing, there is |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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377 a number of methods to "reduce" or "project" a k-dim space in a space of 2 or 3 dimensions. |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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378 This is of great help, not only to summarise the data, but also to find similarities, common trends |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
379 between the data (under the hypothesis that similar data are closer in the k-dimension space). |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
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380 |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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381 This tool returns the visualisation of a dimensional reduction using either: |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
382 |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
383 * Principal Components Analysis (PCA) |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
384 * Hierarchical Clustering of Principal Components (HCPC) |
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4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
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diff
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385 * t-distributed Stochastic Neighbor Embedding (t-SNE) |
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0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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386 |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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387 The tool returns in addition the table of the coordinates of the observations (eg RNAseq libraries) |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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388 in the low dim space, which can be used for post-treatment or to further adjust the provided visualisation. |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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389 |
|
4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
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diff
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390 If HCPC is used, this tool can also return the clustering table. It contains two columns of n observations : |
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8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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391 |
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8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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392 * Observation labels |
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8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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393 * Cluster labels |
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8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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394 |
|
0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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395 ** Contrast data with a factor ** |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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396 The tool offers the possibility to colour data points according to the levels of a factor. |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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changeset
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397 To use the option "Factor to contrast data", provide a tabulated-separated, two-column table |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
398 with first column containing the cell/data library identifiers (same identifiers as those |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
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399 provided as column headers in the input data table) and second column containing the corresponding |
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4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
400 factor levels value (if this vector is numerical, then the color palette used is quantitative). |
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8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
401 This table does not need to be sorted in the same order as in the data |
|
0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
402 table. It may also contain more identifiers than those provided in the data table. |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
403 |
|
4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
404 If HCPC visualisation and constrasting data are chosen, an additional text file is given. It contains |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
405 several metrics of external validation of clustering. It will compare the capacity of HCPC clustering |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
406 to recreate classes contained in the factor data file. If the constrasting factor is quantitative, |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff
changeset
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407 the file will be empty. |
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8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
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diff
changeset
|
408 |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
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diff
changeset
|
409 |
|
0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
410 </help> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
411 <citations> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
412 <citation type="bibtex">@Article{, |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
413 title = {Visualizing High-Dimensional Data Using t-SNE}, |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
414 volume = {9}, |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
415 pages = {2579-2605}, |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
416 year = {2008}, |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
417 author = {L.J.P. {van der Maaten} and G.E. Hinton}, |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
418 journal = {Journal of Machine Learning Research}, |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
419 } |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
420 </citation> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
421 <citation type="bibtex">@Article{, |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
422 title = {Accelerating t-SNE using Tree-Based Algorithms}, |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
423 volume = {15}, |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
424 pages = {3221-3245}, |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
425 year = {2014}, |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
426 author = {L.J.P. {van der Maaten}}, |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
427 journal = {Journal of Machine Learning Research}, |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
428 } |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
429 </citation> |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
430 <citation type="bibtex">@Manual{, |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
431 title = {{Rtsne}: T-Distributed Stochastic Neighbor Embedding using |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
432 Barnes-Hut Implementation}, |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
433 author = {Jesse H. Krijthe}, |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
434 year = {2015}, |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
435 note = {R package version 0.15}, |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
436 url = {https://github.com/jkrijthe/Rtsne}, |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
437 } |
|
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
diff
changeset
|
438 </citation> |
|
4
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
439 <citation type="bibtex">@Manual{, |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
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|
440 title = {{ClusterR}: Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans, |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
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diff
changeset
|
441 K-Medoids and Affinity Propagation Clustering}, |
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8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
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diff
changeset
|
442 author = {Lampros Mouselimis}, |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
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diff
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|
443 year = {2019}, |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
3
diff
changeset
|
444 note = {R package version 1.1.9}, |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
parents:
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diff
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|
445 url = {https://github.com/mlampros/ClusterR}, |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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|
446 } |
|
8e17c31c536a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1282ac9de7c926ab251f88afb2453f52c8b14200
artbio
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diff
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|
447 </citation> |
|
0
cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
artbio
parents:
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|
448 </citations> |
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cad0001b9cfb
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 09dcd74dbc01f448518cf3db3e646afb0675a6fe
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449 </tool> |