# HG changeset patch
# User xiaowei
# Date 1617272302 0
# Node ID 5b11b0530ee65dbac26f2d12ee99f75bd095c9a0

GSVA.xml --2021.4.1

diff -r 000000000000 -r 5b11b0530ee6 GSVA.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GSVA.xml	Thu Apr 01 10:18:22 2021 +0000
@@ -0,0 +1,155 @@
+<tool id="GSVA" name="Gene Set Variation Analysis" version="0.1.0">
+    <description>Estimates GSVA enrichment scores</description>
+    <requirements>
+        <requirement type="package" version="1.38.0">bioconductor-GSVA</requirement>
+        <requirement type="package" version="1.0.12">r-pheatmap</requirement>
+        <requirement type="package" version="1.20.3">r-getopt</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript '$__tool_directory__/GSVA.R'
+        --expr '$expression_data'
+        --geneSet '$geneSet'
+        --method '$method'
+        --img_type '$imgfile.img_args.img_type'
+        --img_width '$imgfile.img_args.img_width'
+        --img_height '$imgfile.img_args.img_height'
+        --img_file '$output_img_file'
+        --GSVA_result '$GSVA_result'
+    ]]></command>
+    <inputs>
+        <param name="expression_data" type="data" format="csv" label="Gene expression data" help="An CSV file that is a matrix of expression values where rows correspond to genes and columns correspond to samples." />
+        
+        <param name="geneSet" type="data" format="rdata" label="Gene Sets" help="An rdata file included geneSetCollection object 'geneSet' as name."/>
+        
+        <param name="method" type="select" label="Method" display="radio" help="Supposted four method: GSVA, ssGSEA, z-score and PLAGE. Details in help.">
+            <option value="gsva">GSVA</option>
+            <option value="ssgsea">ssGSEA</option>
+            <option value="zscore">z-score</option>
+            <option value="plage">PLAGE</option>
+        </param>
+        
+        <section name="imgfile" title="Heatmap" expanded="false">
+            <conditional name="img_args">
+                <param name="img_type" type="select" label="Heatmap file type"> 
+                    <option value="PNG" selected="true">PNG</option>
+                    <option value="PDF">PDF</option>
+                    <option value="JPG">JPG</option>
+                </param>
+                
+                <when value="PNG">
+                    <param name="img_width" type="integer" value="480" min="480" label="Img width(px)" />
+                    <param name="img_height" type="integer" value="480" min="480" label="Img height(px)" />
+                </when>
+                
+                <when value="JPG">
+                    <param name="img_width" type="integer" value="480" min="480" label="Img width(px)" />
+                    <param name="img_height" type="integer" value="480" min="480" label="Img height(px)" />
+                </when>
+                
+                <when value="PDF">
+                    <param name="img_width" type="integer" value="7" min="7" label="Img width(inches)" />
+                    <param name="img_height" type="integer" value="7" min="7" label="Img height(inches)" />                
+                </when>
+
+            </conditional>    
+        </section>
+        
+    </inputs>
+    <outputs>
+        <data name="GSVA_result" format="csv" label="GSVA_enrich_result" />
+        <data format="pdf" name="output_img_file" label="GSVA_heatmap">
+            <change_format>
+                <when input="imgfile.img_args.img_type" value="PNG" format="png"/>
+                <when input="imgfile.img_args.img_type" value="JPG" format="jpg"/>
+            </change_format>
+        </data>
+    </outputs>
+	<tests>
+	  <test>
+	    <param name="expression_data" value="gsva_input2_GSE10245.csv" ftype="csv" />
+	    <param name="geneSet" value="GeneSet_from_Msigdb_KEGG.rdata" ftype="rdata" />
+	    <param name="method" value="gsva" />
+	    <section name="imgfile">
+	      <conditional name="img_args">
+	        <param name="img_type" value="PNG" />
+	        <param name="img_width" value="480" />
+	        <param name="img_height" value="480" />
+	      </conditional>
+	    </section>
+	    <output name="GSVA_result" file="GSVA_enrich_result.csv" ftype="csv" />
+	    <output name="output_img_file" file="GSVA_heatmap.png"  ftype="png" />
+	  </test>
+	</tests>
+	
+	
+    <help><![CDATA[
+        
+.. class:: infomark 
+
+**What it does**
+
+Gene Set Variation Analysis (GSVA) is a Gene Set Enrichment (GSE) method that estimates variation of pathway activity over a sample population in an unsupervised manner. 
+
+This tool is built from function `gsva()` bioconductor package `GSVA`, which included four method to analyze microarray and RNG-seq data.
+
+- **GSVA**: GSVA calculates sample-wise gene set enrichment scores as a function of genes inside and outside the gene set, analogously to a competitive gene set test. And it estimates variation of gene set enrichment over the samples independently of any class label.
+
+- **PLAGSE**: Pathway Level analysis  of Gene Expression (PLAGE) standardizes each gene expression profile over the samples and then estimates the pathway activity profiles for each gene set as the coefficients of the first right-singular vector of the singular value.
+
+- **z-score**: The combined z-score method also standardizes each gene expression profile into z-scores and combine the individual gene z-scores per sample to pathway activity profile.
+
+- **ssGSEA**: The ssGSEA method uses the difference in empirical cumulative distribution functions of gene expression rank inside and outside the gene set to calculate an enrichment statistic per sample which is further normalized by the range of values taken throughout all gene sets amd samples.
+
+--------
+
+=========
+**Input**
+=========
+
+
+**Gene expression data** 
+
+The input data is an CSV file, which included a matrix of expression values where rows correspond to genes and columns correspond to samples.
+Recommend gene id is Entrez ID.
+  
+**Gene Sets**
+
+Gene Sets is an rdata file which included object `geneSet` that is geneSetCollection built by `GSEABase` of bioconductor package. You can use 
+GeneSet from Msigdb/KEGG to get this file.
+
+**Method** 
+	
+Method to employ in the estimation of gene-set enrichment scores per sample. By default this is set to `GSVA` and other options are `ssGSEA`, `z-score` or `PLAGE`. The latter two standardize first expression profiles into z-scores over the samples and, in the case of zscore, it combines them together as their sum divided by the square-root of the size of the gene set, while in the case of plage they are used to calculate the singular value decomposition (SVD) over the genes in the gene set and use the coefficients of the first right-singular vector as pathway activity profile.
+
+--------
+
+==========
+**Output**
+==========
+
+**1. A gene-set by sample matrix GSVA enrichment scores**
+
+    ========= ========== ======== ======== ======== ==== =========
+    geneSet     sample_1 sample_2 sample_3 sample_4 ...  sample_n
+    ========= ========== ======== ======== ======== ==== =========
+    pathway_1   
+    pathway_2
+    pathway_3
+    pathway_4
+    ...
+    pathway_n
+    ========= ========== ======== ======== ======== ==== =========
+
+ 
+**2. Heatmap for the matrix GSVA enrichment scores**
+
+ You can define the heatmap file type, width and height in the part of input.
+ 
+    ]]></help>
+
+    <citations>
+        <citation type="doi">10.1186/1471-2105-14-7</citation>
+    </citations>
+    
+
+</tool>
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