<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>