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+++ b/quantp.xml	Fri Sep 14 12:22:31 2018 -0400
@@ -0,0 +1,195 @@
+<tool id="quantp" name="QuanTP" version="1.0.0">
+    <description>Correlation between protein and transcript abundances</description>
+    <requirements>
+        <requirement type="package" version="1.10.4">r-data.table</requirement>
+        <requirement type="package" version="3.0.1">r-gplots</requirement>
+        <requirement type="package" version="0.7.6">r-dplyr</requirement>
+        <requirement type="package" version="3.0.0">r-ggplot2</requirement>
+        <requirement type="package" version="0.4.5">r-ggfortify</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+Rscript '$__tool_directory__/quantp.r' 
+    $experiment_design_option.sample_type 
+    $experiment_design_option.method_type 
+    $experiment_design_option.exp_design 
+    '$pe_exp' 
+    '$te_exp' 
+    $experiment_design_option.correction_method 
+    $cooksd_upper 
+    $nclust 
+    $hm_nclust 
+    $experiment_design_option.volcano_with 
+    '$html_file' 
+    '$html_file.files_path'
+]]></command>
+    <inputs>
+        <param name="pe_exp" type="data" format="tabular" label="Input Protein Abundance File" help="Protein abundance input file"/>
+        <param name="te_exp" type="data" format="tabular" label="Input RNA Abundance File" help="Transcript abundance input file"/>
+        <conditional name="experiment_design_option">
+            <param name="sample_type" type="select" label="Select data input type" help="If the input files already have fold-change values, select Log fold-change. Else, select abundances and the tool will perform the fold-change analysis">
+                <option value="multiple" selected="True">Abundances from different conditions with or without replicates (in multiple columns)</option>
+                <option value="logfold">Log fold-change values (or single condition abundance without replicates in single column) data</option>
+            </param>
+            <when value="logfold">
+                <param name="exp_design" type="hidden" value="none" />
+                <param name="method_type" type="hidden" value="none" />
+                <param name="correction_method" type="hidden" value="none" />
+                <param name="volcano_with" type="hidden" value="pval" />
+            </when>
+            <when value="multiple">
+                <param name="exp_design" type="data" format="tabular" help="Please check the format of the experiment design file">
+                    <label>Experiment design File (Please see the format below)</label>
+                </param>
+                <param name="method_type" type="select" label="Data summarization method" help="Perform T-Test on selecting Mean; Wilcoxon Ranksum Test on selecting Median">
+                    <option value="mean" selected="True">Mean (Default)</option>
+                    <option value="median">Median</option>
+                </param>
+                <param name="correction_method" type="select" label="Multiple testing correction method">
+                    <option value="BH" selected="True">Benjamini and Hochberg (BH) (Default)</option>
+                    <option value="holm">Holm</option>
+                    <option value="hochberg">Hochberg</option>
+                    <option value="hommel">Hommel</option>
+                    <option value="bonferroni">Bonferroni</option>
+                    <option value="BY">Benjamini and Yekutieli (BY)</option>
+                    <option value="none">None</option>
+                </param>
+                <param name="volcano_with" type="select" display="radio" label="Volcano plot with p-value or adjusted p-value">
+                    <option value="pval" selected="True">P-value (Default)</option>
+                    <option value="adj_pval">Adjusted P-value</option>
+                </param>
+            </when>
+        </conditional>
+        <param name="cooksd_upper" type="integer" value="4" optional="false" >
+            <label>Influential Observation cutoff: Observations > value * mean of Cook's distances (Default: "4" * mean(Cook's Distance))</label>
+        </param>
+        <param name="nclust" type="select" label="K-mean clustering: Number of clusters">
+            <option value="1">1</option>
+            <option value="2">2</option>
+            <option value="3">3</option>
+            <option value="4" selected="True">4</option>
+            <option value="5">5</option>
+            <option value="6">6</option>
+            <option value="7">7</option>
+            <option value="8">8</option>
+            <option value="9">9</option>
+            <option value="10">10</option>
+        </param>
+      
+        <param name="hm_nclust" type="select" label="Hierarchical clustering: Number of clusters (from Heatmap)">
+            <option value="1">1</option>
+            <option value="2">2</option>
+            <option value="3">3</option>
+            <option value="4">4</option>
+            <option value="5" selected="True">5</option>
+            <option value="6">6</option>
+            <option value="7">7</option>
+            <option value="8">8</option>
+            <option value="9">9</option>
+            <option value="10">10</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="html" name="html_file" label="protein transcript correlation on ${pe_exp.name} and ${te_exp.name}"/>
+    </outputs>
+    <tests>
+        <test>
+            <conditional name="experiment_design_option">
+                <param name="sample_type" value="multiple"/>
+                <param name="method_type" value="mean"/>
+                <param name="exp_design" value="exp_design_file.tabular" ftype="tabular" />
+                <param name="correction_method" value="BH"/>
+                <param name="volcano_with" value="pval"/>
+            </conditional>
+            <param name="pe_exp" value="protein_data.tabular" ftype="tabular" />
+            <param name="te_exp" value="transcript_data.tabular" ftype="tabular" />
+            <param name="cooksd_upper" value="4"/>
+            <param name="nclust" value="4"/>
+            <param name="hm_nclust" value="5"/>
+            <output name="html_file">
+                <assert_contents>
+                    <has_text text="SAMPLE DISTRIBUTION" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+QuanTP correlates *transcript abundance* and *protein abundance* to examine the association between them.
+
+It either takes in the log fold-change of abundances as input or raw abundances from different conditions where it calculates the log ratios of abundances between two conditions.
+
+Transcript input file can be generated from the quantitative RNA-Seq study whereas Protein input file can be generated from quantitative analysis of mass-spectrometry-based protein data.
+
+-----
+
+**Input file formats**
+
+**Protein data file**
+
+First column - Gene
+
+Following columns - Abundance values (or log fold-change values)
+
+Example of Protein input file
+
+====== ========= ========= ========= ========= ========= ========= ========= =========
+Gene   sample1   sample2   sample3   sample4   sample5   sample6   sample7   sample8
+------ --------- --------- --------- --------- --------- --------- --------- ---------
+GeneX  value     value     value     value     value     value     value     value    
+GeneY  value     value     value     value     value     value     value     value    
+GeneZ  value     value     value     value     value     value     value     value    
+====== ========= ========= ========= ========= ========= ========= ========= =========
+
+
+**Transcript data file**
+
+First column - Gene
+
+Following columns - Abundance values (or log fold-change values)
+
+Example of Transcript input file
+
+====== ========= ========= ========= ========= ========= ========= ========= =========
+Gene   sample1   sample2   sample3   sample4   sample5   sample6   sample7   sample8 
+------ --------- --------- --------- --------- --------- --------- --------- ---------
+GeneX  value     value     value     value     value     value     value     value    
+GeneY  value     value     value     value     value     value     value     value    
+GeneZ  value     value     value     value     value     value     value     value    
+====== ========= ========= ========= ========= ========= ========= ========= =========
+
+
+**Data input type**
+
+If data input type is abundance, experiment design file is required.
+
+Example of experiment design file
+
+======== =========
+case     groupA   
+control  groupB   
+sample1  groupA   
+sample2  groupA   
+sample3  groupA   
+sample4  groupA   
+sample5  groupB   
+sample6  groupB   
+sample7  groupB   
+sample8  groupB   
+======== =========
+
+Note: No title/header in experiment design file and the first two lines of the experiment design must have keyword "case" and "control"
+
+  ]]>
+  </help>
+  <citations>
+        <citation type="bibtex">
+@misc{QuanTP: A software resource for quantitative proteo-transcriptomic comparative data analysis and informatics,
+    author={Praveen Kumar, Priyabrata Panigrahi, James Johnson, Wanda Weber, Subina Mehta, Ray Sajulga, Caleb Easterly, Brian Crooker, Mohammad Heydarian, Krishanpal Anamika, Timothy Griffin, and Pratik Jagtap},
+    year={2018},
+    title={QuanTP}
+}
+        </citation>
+    </citations>
+</tool>