--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/find_pathways.xml	Wed Aug 22 11:09:08 2018 -0400
@@ -0,0 +1,100 @@
+<tool id="find_pathways" name="find pathways (keggrest)" version="2018.08.22">
+    <requirements>
+        <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript $__tool_directory__/keggrest.R  
+        
+        #if $input.ids == "text"
+            --id_list="$input.txt"
+        #else
+            --input="$input.file"
+            --id_column="$input.ncol"
+            --header="$input.header"  
+        #end if
+        
+        --id_type="$ref_ids.id_type"
+        --output="$output1" 
+        --nb_pathways="$nb_pathways"
+        --ref="$ref_ids.ref_file"
+
+    ]]></command>
+    <inputs>
+        <conditional name="input" >
+            <param name="ids" type="select" label="Provide your identifiers" help="Copy/paste or ID list 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 "," 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__"/>
+                        </mapping>
+                    </sanitizer>
+                </param>
+            </when>
+            <when value="file" >
+                <param name="file" type="data" format="txt,tabular" label="Select 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="ref_ids">
+            <param name="id_type" type="select" label="select your identifiers type :">
+                <option value="uniprot">Uniprot Accession number</option>
+                <option value="geneID">Entrez gene ID</option>
+            </param>
+            <when value="uniprot">
+                <param name="ref_file" type="select" label="Select species" >
+                    <options from_data_table="uniprot_kegg_list"/>
+                        <option>Human</option>
+                        <option>Mouse</option>
+                </param>
+            </when>
+            <when value="geneID">
+                <param name="ref_file" type="select" label="Select species" >
+                    <options from_data_table="entrez_kegg_list"/>
+                        <option>Human</option>
+                        <option>Mouse</option>
+                </param>
+            </when>
+        </conditional>
+        <param type="integer" name="nb_pathways" label="Set the number of pathways to keep in result" value="10" help="pathways are sorted by percent of mapping gene by pathway in descending order"/>
+    </inputs>
+    <outputs>
+        <data name="output1" format="tsv" />
+    </outputs>
+    <help><![CDATA[
+        Pathview R script
+        Arguments:
+        --help                  Print this test
+        --input                 tab file
+        --id_list               id list ',' separated
+        --id_type               type of input ids (uniprot_AC or geneID)
+        --id_column             number og column containg ids of interest
+        --org                   organism : Hs , Mm, ...
+        --nb_pathways           number of pathways to return
+        --header                boolean
+        --output                output path
+        --ref                  ref file (l.hsa.gene.RData, l.hsa.up.RData)
+
+        Example:
+        Rscript keggrest.R --input='P31946,P62258' --id_type='uniprot' --id_column 'c1' --header TRUE 
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{githubKEGGREST,
+  author = {LastTODO, FirstTODO},
+  year = {TODO},
+  title = {KEGGREST},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/Bioconductor/KEGGREST},
+}</citation>
+    </citations>
+</tool>
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