<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
<!--Proposed Tool Section: [Utilities]-->
<tool id="SiriusAdapter" name="SiriusAdapter" version="2.3.0">
  <description>Tool for metabolite identification using single and tandem mass spectrometry</description>
  <macros>
    <token name="@EXECUTABLE@">SiriusAdapter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>SiriusAdapter

#if $param_in:
  -in $param_in
#end if
#if $param_out_sirius:
  -out_sirius $param_out_sirius
#end if
#if $param_out_fingerid:
  -out_fingerid $param_out_fingerid
#end if
#if $param_profile:
  -profile
  #if " " in str($param_profile):
    "$param_profile"
  #else
    $param_profile
  #end if
#end if
#if $param_candidates:
  -candidates $param_candidates
#end if
#if $param_database:
  -database
  #if " " in str($param_database):
    "$param_database"
  #else
    $param_database
  #end if
#end if
#if $param_noise:
  -noise $param_noise
#end if
#if $param_ppm_max:
  -ppm_max $param_ppm_max
#end if
#if $param_isotope:
  -isotope
  #if " " in str($param_isotope):
    "$param_isotope"
  #else
    $param_isotope
  #end if
#end if
#if $param_elements:
  -elements     "$param_elements"
#end if
#if $param_number:
  -number $param_number
#end if
#if $param_auto_charge:
  -auto_charge
#end if
#if $param_iontree:
  -iontree
#end if
#if $param_no_recalibration:
  -no_recalibration
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml" optional="False" label="MzML Input file" help="(-in) "/>
    <param name="param_profile" display="radio" type="select" optional="False" value="qtof" label="Specify the used analysis profile" help="(-profile) ">
      <option value="qtof" selected="true">qtof</option>
      <option value="orbitrap">orbitrap</option>
      <option value="fticr">fticr</option>
    </param>
    <param name="param_candidates" type="integer" value="5" label="The number of candidates in the output" help="(-candidates) Default 5 best candidates"/>
    <param name="param_database" type="select" optional="False" value="all" label="search formulas in given database" help="(-database) ">
      <option value="all" selected="true">all</option>
      <option value="chebi">chebi</option>
      <option value="custom">custom</option>
      <option value="kegg">kegg</option>
      <option value="bio">bio</option>
      <option value="natural products">natural products</option>
      <option value="pubmed">pubmed</option>
      <option value="hmdb">hmdb</option>
      <option value="biocyc">biocyc</option>
      <option value="hsdb">hsdb</option>
      <option value="knapsack">knapsack</option>
      <option value="biological">biological</option>
      <option value="zinc bio">zinc bio</option>
      <option value="gnps">gnps</option>
      <option value="pubchem">pubchem</option>
      <option value="mesh">mesh</option>
      <option value="maconda">maconda</option>
    </param>
    <param name="param_noise" type="integer" value="0" label="median intensity of noise peaks" help="(-noise) "/>
    <param name="param_ppm_max" type="integer" value="10" label="allowed ppm for decomposing masses" help="(-ppm_max) "/>
    <param name="param_isotope" display="radio" type="select" optional="False" value="both" label="how to handle isotope pattern data" help="(-isotope) Use 'score' to use them for ranking or 'filter' if you just want to remove candidates with bad isotope pattern. With 'both' you can use isotopes for filtering and scoring (default). Use 'omit' to ignore isotope pattern">
      <option value="score">score</option>
      <option value="filter">filter</option>
      <option value="both" selected="true">both</option>
      <option value="omit">omit</option>
    </param>
    <param name="param_elements" type="text" size="30" value="CHNOP[5]S" label="The allowed elements" help="(-elements) Write CHNOPSCl to allow the elements C, H, N, O, P, S and Cl. Add numbers in brackets to restrict the maximal allowed occurence of these elements: CHNOP[5]S[8]Cl[1]. By default CHNOP[5]S is used">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_number" type="integer" value="10" label="The number of compounds used in the output" help="(-number) "/>
    <param name="param_auto_charge" display="radio" type="boolean" truevalue="-auto_charge" falsevalue="" checked="false" optional="True" label="Use this option if the charge of your compounds is unknown and you do not want to assume [M+H]+ as default" help="(-auto_charge) With the auto charge option SIRIUS will not care about charges and allow arbitrary adducts for the precursor peak"/>
    <param name="param_iontree" display="radio" type="boolean" truevalue="-iontree" falsevalue="" checked="false" optional="True" label="Print molecular formulas and node labels with the ion formula instead of the neutral formula" help="(-iontree) "/>
    <param name="param_no_recalibration" display="radio" type="boolean" truevalue="-no_recalibration" falsevalue="" checked="false" optional="True" label="If this option is set, SIRIUS will not recalibrate the spectrum during the analysis" help="(-no_recalibration) "/>
    <expand macro="advanced_options">
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out_sirius" format="tabular"/>
    <data name="param_out_fingerid" format="tabular"/>
  </outputs>
  <help>Tool for metabolite identification using single and tandem mass spectrometry


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SiriusAdapter.html</help>
</tool>