--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/build_protein_interaction_maps.xml	Fri Mar 01 11:23:22 2019 -0500
@@ -0,0 +1,180 @@
+<tool id="build_protein_interaction_maps" name="Build protein interaction maps" version="2019.03.01">
+    <requirements>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python $__tool_directory__/build_protein_interaction_maps.py 
+            #if $input.ids == "text"
+                --input="$input.txt"
+                --input_type="text"
+            #else
+                --input="$input.file"
+                --ncol="$input.ncol"
+                --header="$input.header"
+                --input_type="file"
+            #end if
+            --database=$database.ref
+            #if $database.ref=="biogrid" 
+                --species="${ filter( lambda x: str( x[3] ) == str( $database.ref_file ), $__app__.tool_data_tables['proteore_biogrid_dictionaries'].get_fields() )[0][2] }"
+            #else 
+                --species="Human"
+            #end if
+
+            #if 'PPI_dictionaries' in str($database.ref_file).split('/') : 
+                --dict_path="$database.ref_file"
+            #else
+                --dict_path="$__tool_data_path__/$database.ref_file"
+            #end if
+
+            #if $input.ids == "file"
+                --network_output="$network_output"
+                --nodes_output="$nodes_output"
+            #else 
+                --network_output="$network_output_from_list"
+                --nodes_output="$nodes_output_from_list"
+            #end if
+            --id_type=$database.id_type
+
+    ]]></command>
+    <inputs>
+        <conditional name="input">
+            <param name="ids" type="select" label="Enter IDs" help="Copy/paste or from a file (e.g. table)">
+                <option value="text">Copy/paste your identifiers</option>
+                <option value="file" selected="true">Input file containing IDs</option>
+            </param>
+            <when value="text">
+                <param name="txt" type="text" label="Copy/paste IDs" help='IDs must be separated by tab, space or carriage return into the form field, for example: P31946 P62258' >
+                    <sanitizer invalid_char="">
+                        <valid initial="string.printable">
+                            <remove value="&apos;"/>
+                        </valid>
+                        <mapping initial="none">
+                            <add source="&apos;" target="__sq__"/>
+                            <add source="&#x20;" target=""/>
+                            <add source="&#xA;" target=""/>
+                            <add source="&#xD;" target=""/>
+                            <add source="&#x9;" target=""/>
+                        </mapping>
+                    </sanitizer>
+                </param>
+            </when>
+            <when value="file" >
+                <param name="file" type="data" format="txt,tabular" label="Select your file" help="" />
+                <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does file contain header?" />
+                <param name="ncol" type="text" value="c1" label="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'>
+                    <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
+                </param>
+            </when>
+        </conditional>
+        <conditional name="database">
+            <param name="ref" type="select" label="Select database">
+                <option value="biogrid">BioGRID</option>
+                <option value="bioplex">Human Bioplex 2.0</option>
+                <option value="humap">Human protein complex Map (Hu.map)</option>
+            </param>
+            <when value="biogrid">
+                <param name="id_type" type="select" label="Type/source of IDs" optional="false" >
+                    <option value="GeneID" >Entrez gene ID</option>
+                </param>
+                <param name="ref_file" type="select" label="Species">
+                    <options from_data_table="proteore_biogrid_dictionaries" />
+                </param>
+            </when>
+            <when value="bioplex">
+                <param name="id_type" type="select" label="Type/source of IDs" optional="false">
+                    <option value="UniProt-AC" selected="True" >UniProt accession number</option>
+                    <option value="GeneID">Entrez gene ID</option>
+                </param>
+                <param name="ref_file" type="select" label="Species">
+                    <options from_data_table="proteore_bioplex_dictionaries" />
+                </param>
+            </when>
+            <when value="humap">
+                <param name="id_type" type="select" label="Type/source of IDs" optional="false" >
+                    <option value="GeneID" >Entrez gene ID</option>
+                </param>
+                <param name="ref_file" type="select" label="Species">
+                    <options from_data_table="proteore_humap_dictionaries" />
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="network_output_from_list" format="tsv" label="Network_${database.ref}_from_ids_list">
+            <filter>input['ids'] == "text" </filter>
+        </data>
+        <data name="network_output" format="tsv" label="Network_${database.ref}_from_${input.file.name}">
+            <filter>input['ids'] == "file" </filter>
+        </data>
+        <data name="nodes_output_from_list" format="tsv" label="Nodes_${database.ref}_from_ids_list">
+            <filter>input['ids'] == "text"</filter>
+        </data>
+        <data name="nodes_output" format="tsv" label="Nodes_${database.ref}_from_${input.file.name}">
+            <filter>input['ids'] == "file"</filter>
+        </data>
+    </outputs>
+    <help><![CDATA[
+**Description**
+
+-----
+
+**Input**
+
+Id list of Entrez gene ID or Uniprot-AC from copy/paste or file
+
+-----
+
+**Parameters**
+
+- **biogrid**
+- **bioplex**
+- **hu.map**
+
+-----
+
+**Output**
+
+- **network_file**
+- **nodes_file**
+
+-----
+
+**Data sources (release date)**
+
+This tool uses the following interactomes:
+
+**biogrid**
+
+- BIOGRID-ORGANISM-Homo_sapiens-3.5.167.tab2.txt
+- BIOGRID-ORGANISM-Mus_musculus-3.5.167.tab2.txt
+- BIOGRID-ORGANISM-Rattus_norvegicus-3.5.167.tab2.txt
+- NCBI2Reactome.txt: 'https://www.reactome.org/download/current/NCBI2Reactome.txt'
+
+from https://downloads.thebiogrid.org/BioGRID/Release-Archive/BIOGRID-3.5.167/
+
+**bioplex**
+
+- BioPlex_interactionList_v4a.tsv: http://bioplex.hms.harvard.edu/data/BioPlex_interactionList_v4a.tsv
+- UniProt2Reactome.txt: https://downloads.thebiogrid.org/BioGRID/Release-Archive/BIOGRID-3.5.167/
+- NCBI2Reactome.txt: 'https://www.reactome.org/download/current/NCBI2Reactome.txt'
+
+**Human protein complex Map (Hu.map)
+
+- nodeTable.txt: http://proteincomplexes.org/static/downloads/nodeTable.txt
+- pairsWprob: http://proteincomplexes.org/static/downloads/pairsWprob.txt
+- NCBI2Reactome.txt: 'https://www.reactome.org/download/current/NCBI2Reactome.txt'
+
+-----
+
+.. class:: infomark
+
+**Authors**
+
+David Christiany, 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, FR
+
+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>
+</tool>
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