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<tool id="retr_pepatlas1" name="Get MS/MS observations in tissue/fluid" version="2019.02.26">
    <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([str(ref) if "peptide_atlas" in str(ref).split("/") else $__tool_directory__+"/"+str(ref) for ref in str($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'>
                    <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>
        <!-- Peptide Atlas options -->
        <param name="atlas" type="select" display="checkboxes" multiple="true" label="Proteomics dataset (biological sample)" optional="false" >
            <options from_data_table="proteore_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 - date of downloading)": available human biological samples (tissue/organ/body fluid) analyzed by MS/MS and processed by Peptide Atlas are the following: adrenal gland, brain, breast, CSF (cerebrospinal fluid), colon cancer, digestive system, female and male reproductive system, heart, kidney, liver, lung, pancreas, plasma (non-glycosylated), spleen, testis, urinary bladder, urine. 

----

**Output**

Additional columns are created for each selected proteomics sample reporting the total number of observation (called "ProteinProphet-adjusted N Obs") of all peptides detected by LC-MS/MS and assigned to a protein 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 source (release date)" - replace "MS/MS Proteomics dataset (also called "build") were retrieved from Peptide Atlas website through their query interface (in January 2019) with name and release date as follow:

- Human Adrenal Gland 2014-08
- Human Brain 2015-01
- Human Breast 2014-08
- Human CSF 2014-09
- Human Colon Cancer 2013-02
- Human Digestive System 2014-08
- Human Female Reproductive System 2014-08
- Human Heart 2014-08
- Human Kidney 2014-08
- Human Liver 2014-08
- Human Lung 2014-08
- Human Male Reproductive System 2014-08
- Human Pancreas 2014-08
- Human Plasma Non-Glyco 2017-04
- Human Spleen 2014-08
- Human Testis 2017-01
- Human Urinary Bladder 2014-08
- Human Urine 2014-08

----

.. 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 [e-mail] for any questions or concerns about the Galaxy implementation of this tool.
 
    ]]></help>
    <citations>
    </citations>
</tool>