<tool id="sirius_csifingerid" name="SIRIUS-CSI:FingerID"
      version="4.0.1+galaxy2">
    <description>is used to identify metabolites using single and
        tandem mass spectrometry</description>
    <requirements>
        <requirement type="package" version="4.0.1">
            sirius-csifingerid</requirement>
    </requirements>
    <command detect_errors="exit_code">
    <![CDATA[

        python '$__tool_directory__/sirius_csifingerid.py'
            --input_pth '$input'
            --database $database
            --profile $profile
            --candidates $candidates
            --ppm_max $ppm_max
            --polarity $polarity
            --out_dir .
            --result_pth sirius_all_summary.tsv
            --cores_top_level 1
            --meta_select_col $meta_select_col
            --minMSMSpeaks $minMSMSpeaks
            --schema $schema
            --temp_dir .

    ]]></command>
    <inputs>
        <param name="input" argument="--input_pth" type="data" format="msp"
               label="MSP file (output from Create MSP tool)" />
        <param argument="--database" type="select"
               label="Select SIRIUS-CSI:FingerID Database" >
            <option value="PubChem" >PubChem</option>
            <option selected="true" value="hmdb">HMDB</option>
            <option value="kegg">KEGG</option>
            <option value="knapsack">KNApSAcK</option>
            <option value="biocyc">BioCyc</option>
            <option  value="all">All (see help)</option>
        </param>
        <param argument="--ppm_max" type="integer" value="10" min="0"
               label="Mass deviation of the fragment peaks in ppm" />
        <param argument="--candidates" type="integer" value="5" min="1"
               label="Maximum number of candidates in the output" />
        <param argument="--polarity" type="select" label="Ion mode" >
            <option value="positive" selected="true">Positive</option>
            <option value="negative">Negative</option>
        </param> 
        <param argument="--profile" type="select" label="Analysis used" >
            <option value="orbitrap" selected="true">Orbitrap</option>
            <option value="qtof">qTOF</option>
            <option value="fticr">FT-ICR</option>
        </param>
        <param argument="--schema" type="select" label="Schema"
               help="Schema used for the MSP file (auto will try to
                     determine the schema automatically)">
            <option value="auto" selected="True">Auto</option>
            <option value="msp" >Generic MSP</option>
            <option value="massbank">MassBank</option>
        </param>
        <param argument="--meta_select_col" type="select"
               label="Choose how additional metadata columns are extracted"
               help="The SIRIUS-CSI:Fingerid output can have additional
               metadata columns added; these can be either extracted from all
               MSP parameters or from the 'Name' and 'RECORD_TITLE' MSP
               parameters. Additionally, columns can be added from the 'Name'
               or 'RECORD_TITLE' parameters by splitting on | and :  e.g.
               'MZ:100.2 | RT:20 | xcms_grp_id:1' would create MZ,RT and
               xcms_grp_id columns">
            <option value="name" selected="true">
                Extra metadata columns from the Name or RECORD_TITLE</option>
            <option value="name_split" >
                Extra metadata columns from the Name or
                RECORD_TITLE (each column is split on "|" and ":" ) </option>
            <option value="all">
                Extra metadata columns from all MSP parameters</option>
        </param>
        <param argument="--minMSMSpeaks" type="integer" min="0" value="0"
               label="Minimum number of MS/MS peaks"/>
    </inputs>
    <outputs>
        <data name="results" format="tsv"
              from_work_dir="sirius_all_summary.tsv"/>
    </outputs>
    <tests>
        <test>
            <!-- Test "massbank" style data format  -->
            <param name="input" value="ML006801.txt"  ftype="msp"/>
            <output name="results" file="ML006801.tsv"/>
        </test>
        <test>
            <!-- Test "generic format" style data format  -->
            <param name="input" value="generic.msp" ftype="msp"/>
            <output name="results" file="generic.tsv"/>
        </test>
        <test>
            <!-- Test for glucose (qtof) MassBank data format  -->
            <param name="input" value="RP022611.txt" ftype="msp"/>
            <param name="profile" value="qtof"/>
            <output name="results" file="RP022611_result.tsv"/>
        </test>
        <test>
            <!-- Test for glucose (q-exactive) GNPS, MoNA data format  -->
            <param name="input" value="CCMSLIB00000578155.msp" ftype="msp"/>
            <param name="profile" value="orbitrap"/>
            <output name="results" file="CCMSLIB00000578155_result.tsv"/>
        </test>
        <test>
            <!-- Test invalid adduct  -->
            <param name="input" value="invalid_adduct.msp" ftype="msp"/>
            <output name="results" file="invalid_adduct_result.tsv"/>
        </test>
    </tests>
    <help>
----------------
SIRIUS-FingerID
----------------

Description
-----------

| SIRIUS is a java-based software framework for discovering a landscape of
| de-novo identification of metabolites using single and tandem mass
| spectrometry. SIRIUS uses isotope pattern analysis for detecting the
| molecular formula and further analyses the fragmentation pattern of a
| compound using fragmentation trees. Website:
| https://bio.informatik.uni-jena.de/software/sirius/
|

Parameters
----------

**\1. MSP file**

MSP file created using *Create MSP* tool

**\2. Select SIRIUS-CSI:FingerID Databases**

The following databases are available:

* PubChem

* HMDB

* KEGG

* KNApSAcK

* BioCyc

* All (SIRIUS will consider all m/z possible molecular formulas) 

**\3. Mass deviation of the fragment peaks in ppm**

Allowed mass deviation of the fragment peaks.

**\4. The maximum number of candidates in the output**

Set the top X candidates to return.

**\5. Ion mode**

* Positive

* Negative

**\6. Analysis used**

* Orbitrap

* qTOF

* FT-ICR

If you want to analyze spectra measured with Orbitrap or FT-ICR, you should
specify the appropriate analysis profile. A profile is a set of configuration
options and scoring functions SIRIUS 3 will use for its analysis. For example,
the Orbitrap and FT-ICR profiles have tighter constraints for the allowed mass
deviation but do not rely so much on the intensity of isotope peaks.


Developers and contributors
---------------------------

- **Jordi Capellades (j.capellades.to@gmail.com) - Universitat Rovira i Virgili (SP)**
- **Thomas N Lawson (t.n.lawson@bham.ac.uk) - University of Birmingham (UK)**
- **Simon Bray (sbray@informatik.uni-freiburg.de) - University of Freiburg (Germany)**
- **Ralf Weber (r.j.weber@bham.ac.uk) - University of Birmingham (UK)**

    </help>
    <citations>
        <citation type="doi">10.1073/pnas.1509788112</citation>
        <citation type="doi">10.1093/bioinformatics/btu275</citation>
    </citations>
</tool>