--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster_profiler.xml	Wed Aug 22 10:44:46 2018 -0400
@@ -0,0 +1,249 @@
+<tool id="cluter_profiler" name="clusterProfiler" version="2018.08.22">
+    <description>
+    GO terms classification and enrichment analysis
+    </description>
+    <requirements>
+        <requirement type="package" version="3.4.1">R</requirement>
+        <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement>
+        <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement>
+        <requirement type="package" version="3.2.0">bioconductor-dose</requirement>
+        <requirement type="package" version="3.4.4">bioconductor-clusterprofiler</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript "$__tool_directory__/GO-enrich.R"
+        #if $input.ids == "text"
+            --input_type="text"
+            --input="$input.txt"
+        #else
+            --input_type="file"
+            --input="$input.file"
+            --ncol="$input.ncol"
+            --header="$input.header"
+        #end if
+        
+        --id_type="$idti.idtypein"
+
+        --species="$species"
+
+        #if $ggo.go_represent == "true"
+            --go_represent="true"
+            --level="$ggo.level"
+        #else
+            --go_represent="false"
+        #end if
+
+        #if $ego.go_enrich == "true"
+            --go_enrich="true"
+            --pval_cutoff="$ego.pval"
+            --qval_cutoff="$ego.qval"
+            #if $ego.universe.universe_option == "true"
+            #if $ego.universe.universe_input.universe_ids == "text"
+                --universe_type="text"
+                --universe="$ego.universe.universe_input.txt"
+            #else
+                --universe_type="file"
+                --universe="$ego.universe.universe_input.file"
+                --uncol="$ego.universe.universe_input.ncol"
+                --uheader="$ego.universe.universe_input.header"
+            #end if
+            --universe_id_type="$ego.universe.universe_idti.universe_idtypein"
+        #end if
+        #else
+            --go_enrich="false"
+        #end if
+        
+        --onto_opt="$ontology"
+
+        --text_output="$text_output"
+    ]]></command>
+    <inputs>
+        <conditional name="input" >
+            <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list (Uniprot accession Nb or Entrez Gene ID) from a file (e.g. table)" >
+                <option value="text">Copy/paste your identifiers</option>
+                <option value="file" selected="true">Input file containing your identifiers</option>
+            </param>
+            <when value="text" >
+                <param name="txt" type="text" label="Copy/paste your identifiers" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
+                    <sanitizer>
+                        <valid initial="string.printable">
+                            <remove value="&apos;"/>
+                        </valid>
+                        <mapping initial="none">
+                            <add source="&apos;" target="__sq__"/>
+                        </mapping>
+                    </sanitizer>
+                </param>
+            </when>
+            <when value="file" >
+                <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your list of IDs" help="" />
+                <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
+                <param name="ncol" type="text" value="c1" label="The column number of IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />                
+            </when>
+        </conditional>
+        <conditional name="idti" >
+            <param name="idtypein" type="select" label="Select type/source of identifier of your list" help="Please see example of IDs in help section" >
+                <option value="Uniprot">UniProt accession number (e.g. P31946)</option>
+                <option value="Entrez">Entrez Gene ID (e.g : 4151)</option>
+            </param>
+            <when value="Uniprot"/>
+            <when value="Entrez"/>
+        </conditional>
+            
+        <param name="species" type="select" label="Select a species" >
+            <option value="human">Human</option>
+            <option value="mouse">Mouse</option>
+            <option value="rat">Rat</option>
+        </param>
+        <conditional name="ggo">
+            <param name="go_represent" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Do you want to perform GO categories representation analysis?"/>
+            <when value="true">
+                <param name="level" type="select" label="Level of the ontology at which the profile has to be built (the higher this number, the deeper the GO level)">
+				    <option value="1">1</option>
+				    <option value="2">2</option>
+				    <option value="3" selected="True">3</option>
+			    </param>
+            </when>
+            <when value="false"/>
+        </conditional>
+        <conditional name="ego">
+            <param name="go_enrich" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Do you want to perform GO categories enrichment analysis?"/>
+            <when value="true">
+                <param name="pval" type="float" value="0.01" label="P-value cut off"/>
+			    <param name="qval" type="float" value="0.05" label="Q-value cut off"/>
+                <conditional name="universe" >
+                    <param name="universe_option" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Would you like to define your own background IDs?"/>
+                    <when value="true">
+                        <conditional name="universe_input">
+                            <param name="universe_ids" type="select" label="Provide your background IDs list" help="Copy/paste or ID list (Uniprot accession Nb or Entrez Gene ID) from a file (e.g. table)" >
+                                <option value="text">Copy/paste your background identifiers</option>
+                                <option value="file" selected="true">Input file containing your background identifiers</option>
+                            </param>
+                            <when value="text" >
+                                <param name="txt" type="text" label="Copy/paste your background identifiers" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
+                                    <sanitizer>
+                                        <valid initial="string.printable">
+                                            <remove value="&apos;"/>
+                                        </valid>
+                                        <mapping initial="none">
+                                            <add source="&apos;" target="__sq__"/>
+                                        </mapping>
+                                    </sanitizer>
+                                </param>
+                            </when>
+                            <when value="file" >
+                                <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your background IDs list" help="" />
+                                <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
+                                <param name="ncol" type="text" value="c1" label="The column number of IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />                
+                            </when>
+                        </conditional>
+                        <conditional name="universe_idti" >
+                            <param name="universe_idtypein" type="select" label="Select type/source of background identifier of your list" help="Please see example of IDs in help section" >
+                                <option value="Uniprot">UniProt accession number</option>
+                                <option value="Entrez">Entrez Gene ID</option>
+                            </param>
+                            <when value="Uniprot"/>
+                            <when value="Entrez"/>
+                        </conditional>
+                    </when>
+                    <when value="false"/>
+                </conditional>
+            </when>
+            <when value="false"/>
+        </conditional>
+				
+		<param name="ontology" type="select" display="checkboxes" multiple="true" label="Please select GO terms category">
+            <option value="CC">Cellular Component</option>
+            <option value="BP">Biological Process</option>
+            <option value="MF">Molecular Function</option>
+        </param>
+	    
+	    
+	    
+    </inputs>
+    <outputs>
+        <data name="text_output" format="tabular" label="clusterProfiler text output" />
+        <collection type="list" label="clusterProfiler diagram outputs" name="output" >
+	    <discover_datasets pattern="(?P&lt;designation&gt;.+\.png)" ext="png" />
+	</collection>
+    </outputs>
+    <tests>
+        <test>
+            <conditional name="input">
+                <param name="ids" value="file"/>
+                <param name="file" value="Lacombe_et_al_2017_OK.txt"/>
+                <param name="header" value="true"/>
+                <param name="ncol" value="c1"/>
+            </conditional>
+            <conditional name="idti">
+                <param name="idtypein" value="Uniprot"/>
+            </conditional>
+            <param name="species" value="human"/>
+            <conditional name="ggo">
+                <param name="go_represent" value="true"/>
+                <param name="level" value="3"/>
+            </conditional>
+            <conditional name="ego">
+                <param name="go_enrich" value="false"/>
+            </conditional>
+            <param name="ontology" value="CC"/>
+            <output name="text_output" file="clusterProfiler_text_output.tabular"/>
+            <output_collection name="output">
+                <element name="GGO.CC.png" file="GGO.CC.png" ftype="png"/>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+       
+**Galaxy component based on R package clusterProfiler (see ref below)**
+ 	
+This component allows to perform GO enrichment-analyses.
+
+Given a list of IDs, the tool either 
+  (i)  performs gene classification based on GO distribution at a specific level, or
+  (ii) calculates GO categories enrichment (over- or under-representation) for the IDs of the input list, compared to a background. 
+	User has the possibility to use for this background: either the whole organism, or a user-defined list. In this latter case,
+	we recommand to use the "Retrieve tissue-specific expression data" ProteoRE tool to constitute this list according to user
+	parameters. 
+
+**Input required**
+
+This component works with Gene ids (e.g : 4151, 7412) or Uniprot accession number (e.g. P31946). 
+
+Two modes are allowed: either by supplying a tabular file (.csv, .tsv, .txt, .tab) including your IDs (identifiers) 
+or by copy/pasting your IDs (separated by a space).
+
+ 
+**Output**
+
+Text (tables) and graphics representing the repartition and/or enrichment of GO categories. 
+
+**User manual / Documentation** of the clusterProfiler R package (functions and parameters):
+https://bioconductor.org/packages/3.7/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html
+(Very well explained)
+
+**Reference**
+ 
+clusterProfiler R package reference : 
+G Yu, LG Wang, Y Han, QY He. clusterProfiler: an R package for comparing biological themes among gene clusters. 
+OMICS: A Journal of Integrative Biology 2012, 16(5):284-287. 
+doi:[10.1089/omi.2011.0118](http://dx.doi.org/10.1089/omi.2011.0118)
+
+-----
+
+.. class:: infomark
+
+**Galaxy integration**
+
+T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
+
+Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
+
+This work has been partially funded through the French National Agency for Research (ANR) IFB project.
+
+Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
+
+
+    ]]></help>
+    <citations>
+    </citations>
+</tool>