--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sPLS.xml	Fri Jun 18 20:23:19 2021 +0000
@@ -0,0 +1,464 @@
+<tool id="secimtools_spls" name="Metabolite - Gene Integration" version="@WRAPPER_VERSION@">
+  <description></description>
+  <macros>
+      <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <stdio> 
+    <exit_code range="2" level="fatal" description="Not enough metabolites for the Analysis."/> 
+  </stdio> 
+  <command detect_errors="exit_code"><![CDATA[
+    sPLS.py
+      -g=$metsOption.geneDataset
+      -gid=$metsOption.geneId
+      #if $metsOption.useGeneAnnoCond.useGeneAnno == "y":
+        -ga=$metsOption.useGeneAnnoCond.geneAnno
+        -gn=$metsOption.useGeneAnnoCond.geneName
+      #end if
+      -go=$metsOption.genesOption.allGenes
+      #if $metsOption.genesOption.allGenes == "geneList":
+        -gl=$metsOption.genesOption.relatedGeneList
+      #end if
+      #if $metsOption.genesOption.allGenes == "path":
+        -gkp=$metsOption.genesOption.geneKeggPath
+        -mkp=$metsOption.genesOption.metKeggPath
+      #end if
+      #if $metsOption.genesOption.allGenes == "pana":
+        -gka=$metsOption.genesOption.geneKeggAnno
+        -gkn=$metsOption.genesOption.geneKeggName
+        -p2g=$metsOption.genesOption.path2genes
+        -cu=$metsOption.genesOption.cutoff
+        -f=$metsOption.genesOption.facSel
+        #if $metsOption.genesOption.PANAAnno.usePANAAnno == "yes":
+          -p2n=$metsOption.genesOption.PANAAnno.path2names
+        #end if
+        -o3=$panaOut
+      #end if
+      -k=$keepX
+      -t=$threshold
+      -m=$metDataset
+      -mid=$metId
+      #if $useMetAnnoCond.useMetAnno == "y":
+        -ma=$useMetAnnoCond.metAnno
+        -mn=$useMetAnnoCond.metName
+      #end if
+      -mo=$metsOption.allMets
+      -mka=$metsOption.metKeggAnno
+      #if $metsOption.allMets == "mmc":
+        -d=$metsOption.design
+        -c=$metsOption.corr
+        -sl=$metsOption.sigmaLow
+        -sh=$metsOption.sigmaHigh
+        -sn=$metsOption.sigmaNum
+        -f2=$figure2
+        -o2=$mmcOut
+      #end if
+      #if $metsOption.allMets == "both":
+        -d=$metsOption.design
+        -c=$metsOption.corr
+        -sl=$metsOption.sigmaLow
+        -sh=$metsOption.sigmaHigh
+        -sn=$metsOption.sigmaNum
+        -f2=$figure2
+        -o2=$mmcOut
+      #end if
+      -f1=$figure1
+      -o1=$splsOut
+  ]]></command>
+  <inputs>
+    <param name="metDataset" type="data" format="tabular" label="Metabolite Wide Dataset for Integration" help="Select the Metabolite Wide Dataset from your history"/>
+    <param name="metId" type="text" size="30" value="" label="Unique Metabolite FeatureID" help="Name of the column in your Metabolite Wide Dataset that contains unique identifiers."/> 
+    <conditional name="useMetAnnoCond">
+      <param name="useMetAnno" type="select" label="Use Metabolite Annotation File?" help="You can chose to input a file containing metabolite annotation information (e.g. metabolite names, identifiers, etc.) to use for labeling the output files.">
+        <option value="n">No</option>
+        <option value="y">Yes</option>
+      </param>
+      <when value="y">
+        <param name="metAnno" type="data" format="tabular" label="Metabolomic Annotation File" help="Select the Metabolomic Annotation File from your history."/>
+        <param name="metName" type="text" size="30" value="" label="Metabolite Names" help="Name of the column in your Metabolomic Annotation Dataset that contains metabolite annotation information."/> 
+      </when>
+    </conditional> 
+    <conditional name="metsOption">
+      <param name="allMets" type="select" display="radio" label="Select which option to use for subsetting the Metabolite Wide Dataset" help="Select one of the options above.">
+        <option value="generic">By metabolite class -- Uses the 'Name_in_KEGG' column generated from the 'Link Name to KEGGID' tool to subset.</option>
+        <option value="mmc">By MMC pattern -- Runs the SECIMTools MMC tool and uses the tool-generated pattern blocks for subseting.</option>
+        <option value="both">By both metabolite class AND by MMC pattern.</option>
+      </param>
+      <when value="generic">
+        <param name="metKeggAnno" type="data" format="tabular" label="'Metabolite to KEGGID Link' File."  help="Select the 'Metabolite to KEGGID Link' File from your history. This file can be generated using the 'Link Name to KEGGID' tool."/>
+        <param name="geneDataset" type="data" format="tabular" label="Gene Expression Wide Dataset for Integration" help="Select the Gene Expression Wide Dataset from your history"/>
+        <param name="geneId" type="text" size="30" value="" label="Unique Gene FeatureID" help="Name of the column in your Gene Expression Wide Dataset that contains unique identifiers."/>
+        <conditional name="useGeneAnnoCond">
+          <param name="useGeneAnno" type="select" label="Use a Gene Annotation File?" help="You can chose to input a file containing gene annotation information (e.g. gene names, identifiers, etc.) for labeling the output files.">
+            <option value="n">No</option>
+            <option value="y">Yes</option>
+          </param>
+          <when value="y">
+            <param name="geneAnno" type="data" format="tabular" label="Gene Expression Annotation File" help="Select the Gene Expression Annotation File from your history."/>
+            <param name="geneName" type="text" size="30" value="" label="Gene Names" help="Name of the column in your Gene Expression Annotation Dataset that contains gene annotation information."/> 
+          </when>
+        </conditional>   
+        <conditional name="genesOption">
+          <param name="allGenes" type="select" display="radio" label="Select which option to use for subsetting the Gene Expression Wide Dataset" help="Select one of the options above.">
+            <option value="all">Include all genes in the Gene Expression Wide Dataset -- no subsetting.</option>
+            <option value="geneList">Use a custom tsv file containing specific genes of interest.</option>
+            <option value="path">Include genes linked to each metabolite class through common KEGG pathways.</option>
+            <option value="pana">Use Metagenes from PANA (PAthway Network Analysis from gene expression data).</option>
+          </param>
+          <when value="geneList">
+            <param name="relatedGeneList" type="data" format="tabular" label="Select a Custom Gene List from your history" help="This custom list must consist of a single column of Gene Symbols."/>
+          </when>
+          <when value="path">
+            <param name="geneKeggPath" type="data" format="tabular" label="Gene Expression KEGG Pathway File" help="Select the Gene Expression KEGG Pathway File from your history. This file can be generated using the 'Add KEGG Pathway Information' tool."/>
+            <param name="metKeggPath" type="data" format="tabular" label="Metabolomic KEGG Pathway File" help="Select the Metabolomic KEGG Pathway File from your history. This file can be generated using the 'Add KEGG Pathway Information' tool."/>
+          </when>
+          <when value="pana">
+            <param name="geneKeggAnno" type="data" format="tabular" label="Gene to KEGGID Link File" help="Select the Gene to KEGGID Link File from your history. This file can be generated from the 'Link Name to KEGGID' tool."/>
+            <param name="geneKeggName" type="text" label="Gene Symbol" help="Name of the column in your 'Gene to KEGGID Link File' that contains Gene Symbols."/>
+            <param name="path2genes" type="data" format="tabular" label="GeneKEGGID2PathwayID" help="Select the File from your history containing the list of ALL Gene KEGGIDs to Pathway IDs. This file can be generated from the 'Add KEGG Pathway Information' tool."/>
+            <param name="facSel" type="select" display="radio" label="Criterion to select components" help="Choose the criterion to select components. Default: single%.">
+              <option value="single">single% -- Percent of variability for a given principle component.</option>
+              <option value="accum">%accum -- Percent of accumulated variability.</option>
+              <option value="abs.val">abs.val -- Absolute value of the variabily for a given principle component.</option>
+              <option value="rel.abs">rel.abs -- Fold variability of tot.var/rank(X).</option>
+            </param>
+            <param name="cutoff" type="float" value="0.20" label="Variability cut-off value" help="Select the variability cut-off value. Default: 0.20"/>
+            <conditional name="PANAAnno">
+            	<param name="usePANAAnno" type="select" label="Include Pathway Names in results files and figures?" help="You can chose to input a file containing annotations for the KEGG pathwayIDs.">
+            		<option value="no">No</option>
+            		<option value="yes">Yes</option>
+          		</param>
+          		<when value="yes">
+            		<param name="path2names" type="data" format="tabular" label="Pathway Names File" help="Select the Pathway Names File from your history.  This file can be generated from the 'Add KEGG Pathway Information' tool."/>
+            	</when>
+            </conditional>
+          </when>
+        </conditional>
+      </when>
+      <when value="mmc">
+        <param name="metKeggAnno" type="data" format="tabular" label="Metabolite to KEGGID Link File to Input into MMC" help="Select the Metabolite KEGGID Link File from your history.  This file can be generated from the 'Link Name to KEGGID' tool."/>
+        <param name="design" type="data" format="tabular" label="Design Dataset" help="Select the Design file to use with your Metabolite KEGGID Link File. This file can be generated using the 'Create: Design, Wide, and Annotation datasets' tool. Note that you need a column called 'sampleID' that contains the names of your samples."/>
+        <param name="sigmaLow" type="float" size="6" value="0.05" label="Lower sigma bound" help="Default: 0.05." />
+        <param name="sigmaHigh" type="float" size="6" value="0.50" label="Upper sigma bound" help="Default: 0.50." />
+        <param name="sigmaNum" type="integer" size="6" value="451" label="Number of Sigma values" help="Number of values of sigma to search. Default: 451." />
+        <param name="corr" type="select" value="pearson" label="Correlation method" help="Select correlation method for preliminary correlation before clustering. Default: Pearson." >
+          <option value="pearson" selected="true">Pearson</option>
+          <option value="kendall" selected="true">Kendall</option>
+          <option value="spearman" selected="true">Spearman</option>
+        </param>
+        <param name="geneDataset" type="data" format="tabular" label="Gene Expression Wide Dataset for Integration" help="Select the Gene Expression Wide Dataset from your history."/>
+        <param name="geneId" type="text" size="30" value="" label="Unique Gene FeatureID" help="Name of the column in your Gene Expression Annotation File that contains unique identifiers."/>
+        <conditional name="useGeneAnnoCond">
+          <param name="useGeneAnno" type="select" label="Use Gene Annotation File?" help="You can chose to input a file containing gene annotations (e.g. gene names, identifiers, etc.) for labeling output files.">
+            <option value="n">No</option>
+            <option value="y">Yes</option>
+          </param>
+          <when value="y">
+            <param name="geneAnno" type="data" format="tabular" label="Gene Expression Annotation File" help="Select the Gene Expression Annotation File from your history."/>
+            <param name="geneName" type="text" size="30" value="" label="Gene Names" help="Name of the column in your Gene Expression Annotation Dataset that contains gene annotations."/> 
+          </when>
+        </conditional>   
+        <conditional name="genesOption">
+          <param name="allGenes" type="select" display="radio" label="Select which option to use for subsetting the Gene Dataset" help="Select one of the options above.">
+            <option value="all">Include all genes in the Gene Expression Wide Dataset -- no subsetting.</option>
+            <option value="geneList">Use a custom tsv file containing specific genes of interest.</option>
+            <option value="pana">Use Metagenes from PANA (PAthway Network Analysis from gene expression data).</option>
+          </param>
+          <when value="geneList">
+            <param name="relatedGeneList" type="data" format="tabular" label="Select a Custom Gene List from your history" help="This custom list must contain Gene Symbol IDs and must be a single column."/>
+          </when>
+          <when value="pana">
+            <param name="geneKeggAnno" type="data" format="tabular" label="Gene to KEGGID Link File" help="Select Gene to KEGGID Link File from your history. This file can be generated from the 'Link Name to KEGGID' tool."/>
+            <param name="geneKeggName" type="text" label="Gene Symbol" help="Name of the column in your 'Gene to KEGGID Link File' that contains Gene Symbols."/>
+            <param name="path2genes" type="data" format="tabular" label="GeneKEGGID2PathwayID" help="Select the File from your history containing the list of ALL Gene KEGGIDs to Pathway IDs. This file can be generated from the 'Add KEGG Pathway Information' tool."/>
+            <param name="facSel" type="select" display="radio" label="Criterion to select components" help="Choose the criterion to select components. Default: single%.">
+              <option value="single">single% -- Percent of variability for a given principle component.</option>
+              <option value="accum">%accum -- Percent of accumulated variability.</option>
+              <option value="abs.val">abs.val -- Absolute value of the variabily for a given principle component.</option>
+              <option value="rel.abs">rel.abs -- Fold variability of tot.var/rank(X).</option>
+            </param>
+            <param name="cutoff" type="float" value="0.23" label="Variability cut-off value" help="Select the variability cut-off value. Default: 0.23"/>
+            <conditional name="PANAAnno">
+            	<param name="usePANAAnno" type="select" label="Include Pathway Names in results files and figures?" help="You can chose to input a file containing annotations for the KEGG pathway IDs.">
+            		<option value="no">No</option>
+            		<option value="yes">Yes</option>
+          		</param>
+          		<when value="yes">
+            		<param name="path2names" type="data" format="tabular" label="Pathway Names File" help="Select the Pathway Names File from your history. This file can be generated from the 'Add KEGG Pathway Information' tool."/>
+            	</when>
+            </conditional>
+          </when>
+        </conditional>
+      </when>
+      <when value="both">
+        <param name="metKeggAnno" type="data" format="tabular" label="Metabolite to KEGGID Link File" help="Select the Metabolite KEGGID Link File from your history.his file can be generated from the 'Link Name to KEGGID' tool."/>
+        <param name="design" type="data" format="tabular" label="Design File" help="Select the Design file to use with your Metabolite KEGGID Link File. This file can be generated using the 'Create: Design, Wide, and Annotation datasets' tool. Note that you need a 'sampleID' column."/>
+        <param name="sigmaLow" type="float" size="6" value="0.05" label="Lower sigma bound" help="Default: 0.05." />
+        <param name="sigmaHigh" type="float" size="6" value="0.50" label="Upper sigma bound" help="Default: 0.50." />
+        <param name="sigmaNum" type="integer" size="6" value="451" label="Number of Sigma values" help="Number of values of sigma to search. Default: 451." />
+        <param name="corr" type="select" value="pearson" label="Correlation method" help="Select correlation method for preliminary correlation prior to clustering. Default: Pearson." >
+          <option value="pearson" selected="true">Pearson</option>
+          <option value="kendall" selected="true">Kendall</option>
+          <option value="spearman" selected="true">Spearman</option>
+        </param>
+        <param name="geneDataset" type="data" format="tabular" label="Gene Expression Wide Dataset for Integration" help="Select Gene Expression Wide Dataset from your history"/>
+        <param name="geneId" type="text" size="30" value="" label="Unique Gene FeatureID" help="Name of the column in your Gene Expression Annotation File that contains unique identifiers."/>
+        <conditional name="useGeneAnnoCond">
+          <param name="useGeneAnno" type="select" label="Use a Gene Annotation File?" help="You can chose to input a file containing gene annotations (e.g. gene names, identifiers, etc.) to use for labeling output files.">
+            <option value="n">No</option>
+            <option value="y">Yes</option>
+          </param>
+          <when value="y">
+            <param name="geneAnno" type="data" format="tabular" label="Gene Expression Annotation File" help="Select the Gene Expression Annotation File from your history."/>
+            <param name="geneName" type="text" size="30" value="" label="Gene Names" help="Name of the column in your Gene Expression Annotation Dataset that contains gene annotations."/> 
+          </when>
+        </conditional>   
+        <conditional name="genesOption">
+          <param name="allGenes" type="select" display="radio" label="Gene Dataset Subsetting Option" help="Select one of the following.">
+            <option value="all">Include all genes in the Gene Expression Wide Dataset -- no subsetting.</option>
+            <option value="geneList">Upload a custion list containing specific genes of interest.</option>
+            <option value="pana">Use Metagenes (PANA Approach).</option>
+          </param>
+          <when value="geneList">
+            <param name="relatedGeneList" type="data" format="tabular" label="Select a Custom Gene List from your history" help="The list must consist of a single column of Gene Symbols."/>
+          </when>
+          <when value="pana">
+            <param name="geneKeggAnno" type="data" format="tabular" label="Gene to KEGGID Link File" help="Select Gene to KEGGID Link File from your history. This file can be generated from the 'Link Name to KEGGID' tool."/>
+            <param name="geneKeggName" type="text" label="Gene Symbol" help="Name of the column in your 'Gene to KEGGID Link File' that contains Gene Symbols."/>
+            <param name="path2genes" type="data" format="tabular" label="Gene Expression KEGG Pathway File" help="Select the File from your history that contains the list of ALL Gene KEGGIDs to PathwayIDs. This file can be generated from the 'Add KEGG Pathway Information' tool."/>
+            <param name="facSel" type="select" display="radio" label="Criterion to select components" help="Choose the criterion to select components. Default: single%.">
+              <option value="single">single% -- Percent of variability for a given principle component.</option>
+              <option value="accum">%accum -- Percent of accumulated variability.</option>
+              <option value="abs.val">abs.val -- Absolute value of the variabily for a given principle componenet.</option>
+              <option value="rel.abs">rel.abs -- Fold variability of tot.var/rank(X).</option>
+            </param>
+            <param name="cutoff" type="float" value="0.23" label="Variability cut-off value" help="Select the variability cut-off value. Default: 0.23"/>
+            <conditional name="PANAAnno">
+            	<param name="usePANAAnno" type="select" label="Include Pathway Names in results files and figures?" help="You can chose to input a file containing annotations for the KEGG pathwayIDs.">
+            		<option value="no">No</option>
+            		<option value="yes">Yes</option>
+          		</param>
+          		<when value="yes">
+            		<param name="path2names" type="data" format="tabular" label="Pathway Names File" help="Select the Pathway Names File from your history. This file can be generated from the 'Add KEGG Pathway Information' tool."/>
+            	</when>
+            </conditional>
+          </when>
+        </conditional>
+      </when>
+    </conditional>
+    <param name="keepX" type="integer" size="30" value="10" label="Number of Genes to Keep in the Model" help="Enter the number of genes to keep for each component in the sPLS analysis."/>
+    <param name="threshold" type="float" size="30" value="0.8" label="Threshold" help="Correlations under this threshold will NOT be included in the ouput file."/>
+  </inputs>
+  <outputs>
+    <data format="pdf" name="figure1" label="${tool.name} on ${on_string}: sPLS Figure"/>
+    <data format="tabular" name="splsOut" label="${tool.name} on ${on_string}: sPLS Correlation Table"/>
+    <data format="pdf" name="figure2" label="${tool.name} on ${on_string}: MMC Figure">
+      <filter>(metsOption['allMets'] == 'mmc') or (metsOption['allMets'] == 'both')</filter>
+    </data>
+    <data format="tabular" name="mmcOut" label="${tool.name} on ${on_string}: MMC Output Table">
+      <filter>(metsOption['allMets'] == 'mmc') or (metsOption['allMets'] == 'both')</filter>
+    </data>
+    <data format="tabular" name="panaOut" label="${tool.name} on ${on_string}: PANA Output Table">
+      <filter>(metsOption['genesOption']['allGenes'] == 'pana')</filter>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <param name="metDataset" value="metabolite_wide_dataset_01fhl.tsv"/>
+      <param name="metId" value="UniqueID"/>
+      <param name="allMets" value="generic"/>
+      <param name="metKeggAnno" value="metabolite_to_keggId_link_01fhl.tsv"/>
+      <param name="metName" value="MetName"/>
+      <param name="geneDataset" value="gene_wide_dataset_01fhl.tsv"/>
+      <param name="geneId" value="UniqueID"/>
+      <param name="allGenes" value="all"/>
+      <param name="keepX" value="10"/>
+      <param name="threshold" value="0.8"/>
+      <output name="splsOut" file="spls_correlation_file_01fhl.tsv"/>
+      <output name="figure1" file="spls_figure_01fhl.pdf"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+
+**Tool Description**
+
+  NOTE: The parameters you select are data dependent.  
+  
+  This tool carries out the integrated analysis of metabolite and gene expression data. Here, metabolite data are considered the dependent (Y) variable 
+  and genes the explanatory variable. The tool allows for several combinations of metabolite and gene models. A note of caution: a complete metabolite 
+  and gene expression dataset with no filtering will be challenging to interpret using this tool.  
+
+  We recommend that both gene expression and metabolite datasets be reduced to reflect a common biological hypothesis before running this tool. For example, 
+  metabolite data can be subset by class (i.e. using the 'Name_in_KEGG' column generated from the 'Link Name  to KEGGID' tool). Users who want to include 
+  similarly behaving compounds without regard to identification or type of compound can estimate modules with the Modulated Modularity Clustering (MMC) tool 
+  (Stone and Ayroles 2009). Each module can be examined separately. Finally, metabolite data can be reduced by using both metabolite class and the MMC tool.  
+  Similarly, gene expression data can be reduced in scope by uploading and using a custom list of genes of interest or by using metagenes as implemented in PANA
+  (Ponzoni et al. 2014).  
+
+  1) Classes of metabolites can be modeled as a function of metagenes.
+  2) Classes of metabolites can be modeled as a function of a set of individual genes.
+  3) Unbiased clusters of metabolites can be modeled as a function of metagenes
+  4) Unbiased clusters of metabolites can be modeled as a function of a set of individual genes.
+
+  The tool executes a partial least squares regression with variable selection (sparse PLS, sPLS) as implemented in the 'mixOmics' package (Rohart F., Gautier, B, Singh, 
+  A and Lê Cao, K. A. mixOmics: an R package for ‘omics feature selection and multiple data integration. On bioRxiv). The mixomics sPLS function is run in ‘classic mode’ 
+  (http://mixomics.org/methods/spls/) with the number of components included in the model set to 2. In addition, the user selects the number of variables (genes) for 
+  each component to use in model construction. 
+
+  This tool needs at least 1 subset with a minimum number of 3 metabolites to run properly. If the user selects subset metabolites by class and no metabolite groups are 
+  identified or small metabolite groups with less than 3 members are found, the tool will stop and a warning message will be generated to try the MMC option instead. 
+  Similarly, if the user selects subset metabolites using MMC clusters and there are no clusters with at least 3 metabolites, the tool will stop and a warning message 
+  will be generated to try the 'by class’ option instead. 
+
+--------------------------------------------------------------------------------
+
+**INPUT**
+
+**Please see the UserGuide for more details regarding tool inputs and options.**
+
+**Metabolite Wide Dataset**  
+  A wide formatted dataset that contains measurements for each sample (samples are in columns):
+
+    +-----------+---------+---------+---------+-----+
+    | FeatureID | sample1 | sample2 | sample3 | ... |
+    +===========+=========+=========+=========+=====+
+    | met_one   | 10      | 20      | 10      | ... |
+    +-----------+---------+---------+---------+-----+
+    | met_two   | 5       | 22      | 30      | ... |
+    +-----------+---------+---------+---------+-----+
+    | met_three | 30      | 27      | 2       | ... |
+    +-----------+---------+---------+---------+-----+
+    | met_four  | 32      | 17      | 8       | ... |
+    +-----------+---------+---------+---------+-----+
+    | ...       | ...     | ...     | ...     | ... |
+    +-----------+---------+---------+---------+-----+
+
+**Unique Metabolite FeatureID**  
+  Name of the column in your Metabolite Wide Dataset that contains unique identifiers.
+
+**Optional - Metabolite Annotation File**
+  A wide format dataset containing metabolite descriptor information (e.g. metabolite names, m/z ratios). The user can chose a column in the Annotation File for labeling output files.
+
+**Optional - Metabolite Names**
+  Column name in the Metabolite Annotation File to use for labeling output files.
+  
+**Data reduction (subsetting) of Metabolite Data**
+  1) By metablite class - uses a predefined grouping of metabolites based on the 'Name_in_KEGG' column in the Metabolite to KEGGID Link File. 
+  2) By MMC pattern - runs the SECIMTools MMC tool and uses the tool-generated pattern blocks for subsetting.  Please see Stone and Ayroles (2009) for MMC options.
+  3) By both metabolite class AND MMC pattern
+
+**Metabolite to KEGGID Link File**
+  This file MUST contain a column called 'Name_in_KEGG' and can be generated using the 'Link Name to KEGGID' tool.
+
+**Gene Expression Wide Dataset**
+  A wide formatted gene expression dataset that contains measurements for each sample:
+
+    +------------+---------+---------+---------+-----+
+    | FeatureID  | sample1 | sample2 | sample3 | ... |
+    +============+=========+=========+=========+=====+
+    | one        | 10      | 20      | 10      | ... |
+    +------------+---------+---------+---------+-----+
+    | two        | 5       | 22      | 30      | ... |
+    +------------+---------+---------+---------+-----+
+    | three      | 30      | 27      | 2       | ... |
+    +------------+---------+---------+---------+-----+
+    | four       | 32      | 17      | 8       | ... |
+    +------------+---------+---------+---------+-----+
+    | ...        | ...     | ...     | ...     | ... |
+    +------------+---------+---------+---------+-----+
+
+**Unique Gene FeatureID**
+  Name of the column in your Gene Expression Wide Dataset that contains unique gene identifiers.
+
+**Optional - Gene Annotation File**
+  A wide format dataset containing gene annotation information (e.g. gene names). The user can chose a column in the Annotation File for labeling output files.
+
+**Optional - Gene Names**
+  Column name in the Gene Annotation File to use for labeling output files.
+
+**Data reduction (subsetting) of Gene Expression Data**
+  1) No subsetting - include all genes in the Gene Expression Wide Dataset
+  2) Use a custom tsv file containing specific genes of interest - select a custom gene list from your history
+  3) Include genes linked to each metabolite class through common KEGG pathways
+  4) Use Metagenes from PANA (PAthway Network Analysis from gene expression data)
+    
+**Gene Expression KEGG Pathway File** 
+  Contains links between gene symbols and KEGG Pathways. Can be generated using the 'Add KEGG Pathway Information' tool
+
+**Metabolomic KEGG Pathway File**
+  Contains links between metabolites and KEGG Pathways. Can be generated using the 'Add KEGG Pathway Information' tool
+
+**Gene to KEGGID Link File**
+  Contains links between gene symbols and KEGGIDs.
+
+**Gene Symbol**
+  Name of the column in your Gene to KEGGID Link File that contains gene symbols
+
+**GeneKEGGID2PathwayID**
+  Contains KEGG links between gene KEGGIDs and KEGG PathwayIDs. Can be generated from the 'Add KEGG Pathway Information' tool
+      
+**Number of Genes to Keep in Model**
+  default: 10.  This is the number of genes to keep for each principle component in the sPLS analysis.
+
+**Threshold**
+  default: 0.8.  Correlations less than this value will NOT be included in the output files.
+
+--------------------------------------------------------------------------------
+
+**OUTPUT**
+
+**For metabolite reduction by metabolite class and all genes:**
+  (1) A PDF containing a sPLS figure for each metabolite class. 
+  (2) A sPLS Correlation TSV file containing the correlations for each metabolite-gene pair and what subset (metabolite class) the pair locate to.
+
+**For metabolite reduction by MMC the following files will be output in addition to files (1) and (2) above**
+  (3) A MMC PDF Figure containing unsorted, sorted and sorted-smoothed heatmaps of the variance-covariance matrixes
+  (4) A MMC Output TSV file containing algorithm summaries in the following columns:
+  
+    (1) Unique metabolite featureID
+    (2) Module:  Contains the module number for each feature calculated by the MMC tool.
+    (3) Entry Index:  Contains the original order of the names of the rows of the input Metabolite Wide Dataset.
+    (4) Degree:  Average of the absolute values of correlations for the given element in a block to other elements within that block.
+    (5) Average Degree:  Average values of the degrees computed above across all elements within the given block.
+
+**For subsetting genes by generating metagenes using PANA the following files will be output in addition to files (1) and (2) above**
+  (5) A PANA Output TSV table containing associations between gene symbols and KEGG pathays.
+
+  ]]>
+  </help>
+  <citations>
+  	<citation type="bibtex">@article{ponzoni2014pathway,
+	title={Pathway network inference from gene expression data},
+	author={Ponzoni, Ignacio and Nueda, Mar{\'\i}a Jos{\'e} and Tarazona, Sonia and G{\"o}tz, Stefan and Montaner, David and Dussaut, Julieta Sol and Dopazo, Joaqu{\'\i}n and Conesa, Ana},
+	journal={BMC systems biology},
+	volume={8},
+	number={2},
+	pages={S7},
+	year={2014},
+	publisher={BioMed Central}
+	}</citation>
+    <citation type="bibtex">@article{dejean2013mixomics,
+    title={mixOmics: Omics data integration project},
+    author={Dejean, Sebastien and Gonzalez, Ignacio and L{\^e} Cao, Kim-Anh and Monget, Pierre and Coquery, J and Yao, F and Liquet, B and Rohart, F},
+    journal={R package},
+    year={2013}
+    }</citation>
+    <citation type="bibtex">@ARTICLE{Kirpich17secimtools,
+    author = {Alexander S. Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi, Alison M. Morse, Lauren M. McIntyre},
+    title = {SECIMTools: A suite of Metabolomics Data Analysis Tools},
+    journal = {BMC Bioinformatics},
+    year = {in press}
+    }</citation>
+    <citation type="bibtex">
+    @article{garcia2010paintomics,
+    title={Paintomics: a web based tool for the joint visualization of transcriptomics and metabolomics data},
+    author={Garc{\'\i}a-Alcalde, Fernando and Garc{\'\i}a-L{\'o}pez, Federico and Dopazo, Joaqu{\'\i}n and Conesa, Ana},
+    journal={Bioinformatics},
+    volume={27},
+    number={1},
+    pages={137--139},
+    year={2010},
+    publisher={Oxford University Press}
+    }</citation>
+  </citations>
+</tool>