--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Get_ms-ms_observations.xml	Tue Dec 18 09:50:50 2018 -0500
@@ -0,0 +1,128 @@
+<tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2018.12.18">
+    <description>[Peptide Atlas]</description>
+    <requirements>
+        <requirement type="package" version="3.4.1">R</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command interpreter="Rscript">
+        $__tool_directory__/Get_ms-ms_observations.R
+        --input_type="$input.ids"
+        #if $input.ids == "list"
+            --input="$input.list"
+        #else
+            --input="$input.file"
+            --column_number="$input.ncol"
+            --header="$input.header"
+        #end if
+        --atlas=${",".join([$__tool_data_path__+"/"+str(ref) for ref in str($atlas).split(",")])}
+        --output="$output"
+    </command>
+
+    <inputs>
+        <conditional name="input" >
+            <param name="ids" type="select" label="Enter your IDs (UniProt Accession number only)" help="Copy/paste or from a file (e.g. table)" >
+                <option value="list">Copy/paste your IDs</option>
+                <option value="file" selected="true">Input file containing your IDs </option>
+            </param>
+            <when value="list" >
+                <param name="list" type="text" label="Copy/paste your IDs" 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="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 of IDs" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />                
+            </when>
+        </conditional>
+        <!-- Peptide Atlas options -->
+        <param name="atlas" type="select" display="checkboxes" multiple="true" label="Proteomics dataset (biological sample)" optional="false" >
+            <options from_data_table="peptide_atlas">
+                <filter type="sort_by" column="2"/>
+            </options>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data name="output" format="tsv" label=""/>
+    </outputs>
+
+    <tests>
+    <test>
+        <conditional name="input">
+            <param name="ids" value="file"/>
+            <param name="file" value="FKW_Lacombe_et_al_2017_OK.txt"/>
+            <param name="ncol" value="c1"/>
+            <param name="header" value="true"/>
+        </conditional>
+
+        <!--${__HERE__} does not work here, you must put absolute path here and in test-data/peptide_atlas.loc -->
+        <param name="atlas" value="${__HERE__}/test-data/Human_Brain_18-07-2018.tsv"/>
+
+        <output name="output" file="PeptideAtlas_output.txt"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+
+**Description**
+
+Given a list of Uniprot accession number this tool indicates the number of times a protein has(ve) been observed in a given sample using LC-MS/MS proteomics approach. 
+Could be of interest for people who wants to know to what extent a protein is detectable (and to roughly estimate its level) in a given sample using MS-based proteomics. 
+
+----
+
+**Input**
+
+A list of Uniprot accession number (e.g. Q12860) provided either in a copy/paste mode or in the form of a file (in this case, it is necessary to specify the column where are your Uniprot accession number). 
+
+If your input file or list contains other type of IDs, please use the ID_Converter tool.
+
+----
+
+**Parameters**
+
+"Proteomics dataset (biological sample)": available human biological samples analyzed by MS/MS are the following: brain, heart, kidney, liver, plasma, urine and cerebrospinal fluid (CSF). 
+
+----
+
+**Output**
+
+Additional columns are created for each selected proteomics sample reporting the number of times all peptides corresponding to a protein have been observed by LC-MS/MS according to Peptide Atlas. 
+
+a “NA” means that no information has been reported suggesting that this protein has not been observed in the sample of interest.
+
+----
+
+**Data source (release date)**
+
+Data were retrieved from Peptide Atlas release (January 2018) through their query interface.
+
+----
+
+.. class:: infomark
+
+**Authors**
+
+T.P. Lien Nguyen, 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>
+    <citations>
+    </citations>
+</tool>
+