<tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.1.1">
    <description>Run an X!Tandem Search</description>
   <requirements>
         <container type="docker">iracooke/protk-1.4.3</container>
        <requirement type="package" version="1.4.3">protk</requirement>
        <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
    </requirements>
    <command>
        #if $database.source_select=="built_in":
            tandem_search.rb -d $database.dbkey 
        #else
            tandem_search.rb -d $database.fasta_file
        #end if

        #if $tandem_params.source_select=="built_in":
            -T $tandem_params.paramskey 
        #else 
            -T $tandem_params.params_file
        #end if


        --var-mods='
        $variable_mods
        #for $custom_variable_mod in $custom_variable_mods:
            ,${custom_variable_mod.custom_mod}
        #end for
        '

        --fix-mods='
        $fixed_mods
        #for $custom_fix_mod in $custom_fix_mods:
            ,${custom_fix_mod.custom_mod}
        #end for
        '

        $input_file -o $output -r 

        --enzyme=$enzyme 

        --precursor-ion-tol-units=$precursor_tolu 
        -v $missed_cleavages 
        -f $fragment_ion_tol 
        -p $precursor_ion_tol
        $allow_multi_isotope_search 
        $acetyl_protein_nterm
        $cleavage_semi
        $keep_spectra
        --threads "\${GALAXY_SLOTS:-12}"

    </command>
    <inputs>
        <conditional name="database">
            <param name="source_select" type="select" label="Database source">
                <option value="built_in">Built-In</option>
                <option value="input_ref" selected="true">Your Upload File</option>
            </param>
            <when value="built_in">
                <param name="dbkey" type="select" format="text" >
                    <label>Database</label>
                    <options from_file="pepxml_databases.loc">
                        <column name="name" index="0" />
                        <column name="value" index="2" />
                    </options>
                </param>
            </when>
            <when value="input_ref">
                <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
            </when>
        </conditional>
        <conditional name="tandem_params">
            <param name="source_select" type="select" label="Baseline Parameters">
                <option value="built_in" selected="true">Built-In</option>
                <option value="input_ref">Custom parameter file</option>
            </param>
            <when value="built_in">
                <param name="paramskey" type="select" format="text" >
                    <label>Paramset</label>
                    <option value="isb_kscore">ISB K-Score (Recommended for TPP)</option>
                    <option value="isb_native">ISB Native</option>
                    <option value="gpm">GPM</option>
                </param>
            </when>
            <when value="input_ref">
                <param name="params_file" type="data" format="xml" label="Custom X!Tandem Parameters" />
            </when>
        </conditional>

        <param name="input_file" type="data" format="mzml,mgf" multiple="false" label="MSMS File" help="A file with MS/MS data"/>

        <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
            clicking to select multiple items">
            <options from_file="tandem_mods.loc">
                <column name="name" index="0" />
                <column name="value" index="2" />
            </options>
        </param>

        <repeat name="custom_variable_mods" title="Custom Variable Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite).">
            <param name="custom_mod" type="text">
            </param>
        </repeat>

        <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
            clicking to select multiple items">
            <options from_file="tandem_mods.loc">
                <column name="name" index="0" />
                <column name="value" index="2" />
            </options>
        </param>

        <repeat name="custom_fix_mods" title="Custom Fixed Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite).">
            <param name="custom_mod" type="text">
            </param>
        </repeat>

        <param name="acetyl_protein_nterm" type="boolean" label="Allow N-terminal protein acetylation as a variable modification" truevalue="-y" falsevalue="" />        
        <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
            <label>Missed Cleavages Allowed</label>
            <option value="0">0</option>
            <option value="1">1</option>
            <option selected="true" value="2">2</option>
        </param>

        <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue=""/>
        <param name="keep_spectra" type="boolean" label="Keep Spectra" help="Include spectra in the output" truevalue="--output-spectra" falsevalue=""/>

        <param name="enzyme" type="select" format="text">
            <label>Enzyme</label>
            <option value="[R]__pc__{P}">argc - [R]|{P}</option>
            <option value="[X]__pc__[D]">aspn - [X]|[D]</option>
            <option value="[FLWY]__pc__{P}">chymotrypsin - [FLWY]|{P}</option>
            <option value="[R]__pc__[X]">clostripain - [R]|[X]</option>
            <option value="[M]__pc__{X}">cnbr - [M]|{X}</option>
            <option value="[AGILV]__pc__{P}">elastase - [AGILV]|{P}</option>
            <option value="[D]__pc__{P}">formicacid - [D]|{P}</option>
            <option value="[DE]__pc__{P}">gluc - [DE]|{P}</option>
            <option value="[E]__pc__{P}">gluc_bicarb - [E]|{P}</option>
            <option value="[W]__pc__[X]">iodosobenzoate - [W]|[X]</option>
            <option value="[K]__pc__{P}">lysc - [K]|{P}</option>
            <option value="[K]__pc__[X]">lysc-p - [K]|[X]</option>
            <option value="[X]__pc__[K]">lysn - [X]|[K]</option>
            <option value="[X]__pc__[AKRS]">lysn_promisc - [X]|[AKRS]</option>
            <option value="[X]__pc__[X]">nonspecific - [X]|[X]</option>
            <option value="[FL]__pc__[X]">pepsina - [FL]|[X]</option>
            <option value="[P]__pc__[X]">protein_endopeptidase - [P]|[X]</option>
            <option value="[E]__pc__[X]">staph_protease - [E]|[X]</option>
            <option value="[FMWY]__pc__{P},[KR]__pc__{P},[X]__pc__[D]">tca - [FMWY]|{P},[KR]|{P},[X]|[D]</option>
            <option value="[KR]__pc__{P}" selected="true">trypsin - [KR]|{P}</option>
            <option value="[FKLMRWY]__pc__{P}">trypsin/chymotrypsin - [FKLMRWY]|{P}</option>
            <option value="[KR]__pc__{P},[M]__pc__{P}">trypsin/cnbr - [KR]|{P},[M]|{P}</option>
            <option value="[DEKR]__pc__{P}">trypsin_gluc - [DEKR]|{P}</option>
        </param>

        <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.5" min="0" max="10000" label="Fragment ion tolerance"/>
        <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" label="Precursor ion tolerance"/>
        <param name="precursor_tolu" type="select" format="text">
            <label>Precursor Ion Tolerance Units</label>
            <option value="ppm">ppm</option>
            <option value="Da">Da</option>
        </param>
        <param name="allow_multi_isotope_search" type="boolean" label="Allow multi-isotope search" help="This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass." truevalue="--multi-isotope-search" falsevalue=""/>
    </inputs>
    <outputs>
        <data format="tandem" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.tandem"/>
    </outputs>
    <tests>
        <!-- Just test that the tool runs and produces vaguely correct output -->
        <test>
            <param name="source_select" value="input_ref"/>
            <param name="fasta_file" value="testdb.fasta" format="fasta"/>
            <param name="input_file" value="tiny.mzML" format="mzml"/>
            <output name="output" format="tandem">
                <assert_contents>
                    <has_text text="tandem-style" />
                </assert_contents>
            </output>
        </test>
    </tests>
  <help>

**What it does**

Runs an MS/MS database search using the X!Tandem search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores.

----

**References**

Please see http://www.thegpm.org/GPM/references.html for details of references describing the X!Tandem search engine.

  </help>

</tool>