Mercurial > repos > artbio > gsc_high_dimensions_visualisation
diff high_dim_visu.xml @ 5:569334568afa draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_high_dimension_visualization commit 1b98c85982a2a9f9df4b318f672b9b68cff66a93"
| author | artbio |
|---|---|
| date | Mon, 02 Sep 2019 04:39:20 -0400 |
| parents | 8e17c31c536a |
| children | 19bef589f876 |
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--- a/high_dim_visu.xml Thu Jul 11 12:31:28 2019 -0400 +++ b/high_dim_visu.xml Mon Sep 02 04:39:20 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="high_dimensions_visualisation" name="Generate PCA, tSNE and HCPC" version="0.9.4"> +<tool id="high_dimensions_visualisation" name="Generate PCA, tSNE and HCPC" version="0.9.5"> <description>from highly dimensional expression data</description> <requirements> <requirement type="package" version="1.6.2=r35h6115d3f_0">r-optparse</requirement> @@ -7,6 +7,7 @@ <requirement type="package" version="0.15=r351he1b5a44_0">r-rtsne</requirement> <requirement type="package" version="0.4.7=r351h6115d3f_0">r-ggfortify</requirement> <requirement type="package" version="1.1.9=r351h0357c0b_0">r-clusterr</requirement> + <!--<requirement type="package" version="1.11.6=r351hc070d10_0">r-data.table</requirement>--> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> @@ -53,6 +54,7 @@ --HCPC_max '$visualisation.HCPC_max' --HCPC_clusterCA '$visualisation.HCPC_clusterCA' --HCPC_kk '$visualisation.HCPC_kk' + --HCPC_cluster_description '$HCPC_cluster_description' #if $visualisation.res_clustering == "yes": --HCPC_clust '$HCPC_clust' #end if @@ -65,7 +67,7 @@ #end if #if $visualisation.visu_choice == "HCPC" and $factor_condition.factor_choice == "Yes": - --mutual_info '$mutual_info' + --HCPC_mutual_info '$HCPC_mutual_info' #end if --pdf_out '$pdf_out' @@ -134,34 +136,43 @@ <param name="HCPC_npc" value="5" type="integer" label="Number of principal components to keep" help="The number of dimensions which are kept for HCPC analysis (default=5)" /> <param name="HCPC_ncluster" value="-1" type="integer" label="Number of clusters in Hierar. Clustering" - help="nb.clust, the number of clusters to consider in the hierarchical clustering. (default : -1, let HCPC to optimize the number)" /> - <param name="HCPC_metric" type="select" label="Dissimilarity metric" help="Metric to be used for calculating dissimilarities between observations, available 'euclidian' or 'manhattan'? " > - <option value="euclidian" selected="true">euclidian</option> + help="nb.clust - an integer. If 0, the tree is cut at the level the user clicks on (not working in Galaxy). If -1, the tree is + automatically cut at the suggested level (see details). If a (positive) integer, the tree is cut with nb.cluters clusters." /> + <param name="HCPC_metric" type="select" label="Dissimilarity metric" help="Metric to be used for calculating dissimilarities between observations, can be 'euclidean' or 'manhattan' " > + <option value="euclidean" selected="true">euclidean</option> <option value="manhattan">manhattan</option> </param> - <param name="HCPC_method" type="select" label="Clustering method" help="Clustering method between 'ward', 'average', 'single', 'complete', 'weighted' " > + <param name="HCPC_method" type="select" label="Clustering method" help="character string defining the clustering method. + The four methods implemented are 'average' ([unweighted pair-]group [arithMetic] average method, aka ‘UPGMA’), + 'single' (single linkage), 'complete' (complete linkage), and 'ward' (Ward's method). + The default with this Galaxy tool is is 'ward'." > <option value="ward" selected="true">ward</option> <option value="average">average</option> <option value="single">single</option> <option value="complete">complete</option> - <option value="weighted">weighted</option> </param> - <param name="HCPC_consol" type="select" label="k-means consolidation" help="If TRUE, a k-means consolidation is performed" > + <param name="HCPC_consol" type="select" label="k-means consolidation" help="a boolean. If TRUE, a k-means consolidation is performed + (consolidation cannot be performed if kk is used and equals a number)." > <option value="TRUE" selected="true">Yes</option> <option value="FALSE">False</option> </param> <param name="HCPC_itermax" value="10" type="integer" label="Maximum number of iterations for consolidation" - help=" (default=10)" /> + help="An integer. The maximum number of iterations for the consolidation. (default=10)" /> <param name="HCPC_min" value="3" type="integer" label="min number of clusters" - help=" The least possible number of clusters suggested (default=3)" /> + help="an integer. The least possible number of clusters suggested. (default=3)" /> <param name="HCPC_max" value="-1" type="text" label="max number of clusters" - help=" The higher possible number of clusters suggested, by default the minimum between 10 and the number of individuals divided by 2. (default=-1)" /> - <param name="HCPC_clusterCA" type="select" label="clusterCA, Clustering against rows or columns" help="default(rows)" > + help="The higher possible number of clusters suggested, by default the minimum between 10 and the number of individuals divided by 2. (default=-1)" /> + <param name="HCPC_clusterCA" type="select" label="cluster.CA, Clustering against rows or columns" + help="A string equals to 'rows' or 'columns' for the clustering of Correspondence Analysis results.default(rows)"> <option value="rows" selected="true">Rows</option> <option value="cols">Columns</option> </param> - <param name="HCPC_kk" value="-1" type="text" label="kk, Number of clusters used in a Kmeans preprocessing " - help="No k-means consolidation is done if a kk value is provided (default=-1)" /> + <param name="HCPC_kk" value="Inf" type="text" label="kk, Number of clusters used in a Kmeans preprocessing " + help="An integer corresponding to the number of clusters used in a Kmeans preprocessing before the + hierarchical clustering; the top of the hierarchical tree is then constructed from this partition. + This is very useful if the number of individuals is high. Note that consolidation cannot be performed + if kk is different from Inf and some graphics are not drawn. Inf is used by default and no preprocessing + is done, all the graphical outputs are then given." /> <param label="Return HCPC clustering table" name="res_clustering" type="select"> <option value="no" selected="True">No</option> <option value="yes">Yes</option> @@ -184,14 +195,18 @@ <data name="table_coordinates" format="tabular" label="Scatter plot coordinates from ${visualisation.visu_choice} of ${on_string}" > <filter>coord == 'yes'</filter> </data> - <data name="mutual_info" format="txt" label="External validation of clustering from ${visualisation.visu_choice} of ${on_string}" > + <data name="HCPC_mutual_info" format="txt" label="External validation of clustering from ${visualisation.visu_choice} of ${on_string}" > <filter>visualisation['visu_choice'] == 'HCPC' and factor_condition['factor_choice'] == 'Yes'</filter> </data> <data name="HCPC_clust" format="tabular" label="Clustering table from ${visualisation.visu_choice} of ${on_string}" > <filter>visualisation['visu_choice'] == 'HCPC' and visualisation['res_clustering'] == 'yes'</filter> </data> + <data name="HCPC_cluster_description" format="tabular" label="Cluster information from ${visualisation.visu_choice}" > + <filter>visualisation['visu_choice'] == 'HCPC' </filter> + </data> </outputs> <tests> + <!-- test first (for developpers) --> <!-- test PCA --> <test> <param name="input" value="cpm_input.tsv" ftype="txt"/> @@ -271,6 +286,7 @@ <param name="HCPC_npc" value="5"/> <param name="HCPC_ncluster" value="-1"/> <output name="pdf_out" file="hcpc.labels.pdf" compare="sim_size" ftype="pdf"/> + <output name="HCPC_cluster_description" file="hcpc.cluster_description.1.tab" ftype="tabular"/> </test> <!-- test factor contrasting on HCPC --> <test> @@ -283,8 +299,9 @@ <param name="factor_choice" value="Yes" /> <param name="factor" value="factor.tsv" ftype="txt"/> <output name="pdf_out" file="hcpc.nolabels.factor.pdf" compare="sim_size" ftype="pdf"/> - <output name="mutual_info" file="hcpc.factor.extval.txt" ftype="txt"/> + <output name="HCPC_mutual_info" file="hcpc.factor.extval.txt" ftype="txt"/> <output name="HCPC_clust" file="hcpc.clusters.tab" ftype="tabular"/> + <output name="HCPC_cluster_description" file="hcpc.cluster_description.1.tab" ftype="tabular"/> </test> <test> <param name="input" value="cpm_input.tsv" ftype="txt"/> @@ -293,6 +310,7 @@ <param name="HCPC_ncluster" value="-1"/> <param name="visu_choice" value="HCPC" /> <output name="pdf_out" file="hcpc.nolabels.pdf" compare="sim_size" ftype="pdf"/> + <output name="HCPC_cluster_description" file="hcpc.cluster_description.1.tab" ftype="tabular"/> </test> <test> <param name="input" value="cpm_input.tsv" ftype="txt"/> @@ -304,6 +322,7 @@ <param name="HCPC_npc" value="4" /> <output name="pdf_out" file="hcpc-2.labels.pdf" ftype="pdf"/> <output name="table_coordinates" file="hcpc-2.coord.tab" ftype="tabular"/> + <output name="HCPC_cluster_description" file="hcpc.cluster_description.4.tab" ftype="tabular"/> </test> <test> <param name="input" value="cpm_input.tsv" ftype="txt"/> @@ -311,11 +330,12 @@ <param name="visu_choice" value="HCPC" /> <param name="coord" value="yes" /> <param name="HCPC_method" value="single"/> - <param name="HCPC_metric" value="euclidian"/> + <param name="HCPC_metric" value="euclidean"/> <param name="HCPC_npc" value="4" /> <param name="HCPC_clusterCA" value="cols" /> <output name="pdf_out" file="hcpc-3.labels.pdf" compare="sim_size" ftype="pdf"/> <output name="table_coordinates" file="hcpc-3.coord.tab" ftype="tabular"/> + <output name="HCPC_cluster_description" file="hcpc.cluster_description.5.tab" ftype="tabular"/> </test> <!-- test t-SNE --> <test>