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<?xml version='1.0' encoding='UTF-8'?>
<tool id="InspectAdapter" name="InspectAdapter" version="1.12.0">
  <description>Annotates MS/MS spectra using Inspect.</description>
  <macros>
    <token name="@EXECUTABLE@">InspectAdapter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>InspectAdapter

-in ${param_in}
-out ${param_out}
${param_inspect_in}
${param_inspect_out}
-inspect_directory ${param_inspect_directory}
-temp_data_directory ${param_temp_data_directory}
-dbs ${param_dbs}
-trie_dbs ${param_trie_dbs}
-new_db ${param_new_db}
-instrument ${param_instrument}
-precursor_mass_tolerance ${param_precursor_mass_tolerance}
-peak_mass_tolerance ${param_peak_mass_tolerance}
${param_list_modifications}
-modifications ${param_modifications}
${param_use_monoisotopic_mod_mass}
-modifications_xml_file ${param_modifications_xml_file}
-cleavage ${param_cleavage}
-inspect_output ${param_inspect_output}
-inspect_input ${param_inspect_input}
${param_multicharge}
-max_modifications_pp ${param_max_modifications_pp}
-tag_count ${param_tag_count}
${param_no_tmp_dbs}
-p_value ${param_p_value}
-contact_name ${param_contact_name}
-contact_institution ${param_contact_institution}
-contact_info ${param_contact_info}
-threads \${GALAXY_SLOTS:-24} 
${param_blind}
${param_blind_only}
-blind:p_value_blind ${param_p_value_blind}
-blind:snd_db ${param_snd_db}
-blind:max_ptm_size ${param_max_ptm_size}
</command>
  <inputs>
    <param name="param_in" type="data" format="mzXML" optional="False" label="input file in mzXML or mzData format.#br#Note: In mode 'inspect_out' an Inspect results file is read." help="(-in)"/>
    <param name="param_inspect_in" type="boolean" truevalue="-inspect_in true" falsevalue="-inspect_in false" checked="false" optional="True" label="if this flag is set the InspectAdapter will read in mzXML,#br#write an Inspect input file and generate a trie database" help="(-inspect_in)"/>
    <param name="param_inspect_out" type="boolean" truevalue="-inspect_out true" falsevalue="-inspect_out false" checked="false" optional="True" label="if this flag is set the InspectAdapter will read in a Inspect results file#br#and write idXML" help="(-inspect_out)"/>
    <param name="param_inspect_directory" type="text" size="20" label="the directory in which Inspect is located" help="(-inspect_directory)"/>
    <param name="param_temp_data_directory" type="text" size="20" label="a directory in which some temporary files can be stored" help="(-temp_data_directory)"/>
    <param name="param_dbs" type="text" size="20" label="name(s) of database(s) to search in (FASTA and SwissProt supported)" help="(-dbs)"/>
    <param name="param_trie_dbs" type="text" size="20" label="name(s) of databases(s) to search in (trie-format)" help="(-trie_dbs)"/>
    <param name="param_new_db" type="text" size="20" label="name of the merged trie database" help="(-new_db)"/>
    <param name="param_instrument" type="select" optional="True" label="the instrument that was used to measure the spectra#br#(If set to QTOF, uses a QTOF-derived fragmentation model,#br#and does not attempt to correct the parent mass.)" help="(-instrument)">
      <option value="ESI-ION-TRAP">ESI-ION-TRAP</option>
      <option value="QTOF">QTOF</option>
      <option value="FT-Hybrid">FT-Hybrid</option>
    </param>
    <param name="param_precursor_mass_tolerance" type="float" value="2.0" label="the precursor mass tolerance" help="(-precursor_mass_tolerance)"/>
    <param name="param_peak_mass_tolerance" type="float" value="1.0" label="the peak mass tolerance" help="(-peak_mass_tolerance)"/>
    <param name="param_list_modifications" type="boolean" truevalue="-list_modifications true" falsevalue="-list_modifications false" checked="false" optional="True" label="show a list of the available modifications" help="(-list_modifications)"/>
    <param name="param_modifications" type="text" size="20" label="the colon-separated modifications; may be#br#&lt;name&gt;,&lt;type&gt;, e.g.: Deamidation,opt or#br#&lt;composition&gt;,&lt;residues&gt;,&lt;type&gt;,&lt;name&gt;, e.g.: H2C2O,KCS,opt,Acetyl or#br#&lt;mass&gt;,&lt;residues&gt;,&lt;type&gt;,&lt;name&gt;, e.g.: 42.0367,KCS,opt,Acetyl or#br#Valid values for type are &quot;fix&quot; and &quot;opt&quot; (default)#br#If you want terminal PTMs, write &quot;cterm&quot; or &quot;nterm&quot; instead of residues" help="(-modifications)"/>
    <param name="param_use_monoisotopic_mod_mass" type="boolean" truevalue="-use_monoisotopic_mod_mass true" falsevalue="-use_monoisotopic_mod_mass false" checked="false" optional="True" label="use monoisotopic masses for the modifications" help="(-use_monoisotopic_mod_mass)"/>
    <param name="param_modifications_xml_file" type="text" size="20" label="name of an XML file with the modifications" help="(-modifications_xml_file)"/>
    <param name="param_cleavage" type="text" size="20" value="Trypsin" label="the enzyme used for digestion" help="(-cleavage)"/>
    <param name="param_inspect_input" type="data" format="data" label="name for the input file of Inspect (may only be used in a full run)" help="(-inspect_input)"/>
    <param name="param_multicharge" type="boolean" truevalue="-multicharge true" falsevalue="-multicharge false" checked="false" optional="True" label="attempt to guess the precursor charge and mass,#br#and consider multiple charge states if feasible" help="(-multicharge)"/>
    <param name="param_max_modifications_pp" type="integer" value="-1" label="number of PTMs permitted in a single peptide." help="(-max_modifications_pp)"/>
    <param name="param_tag_count" type="integer" value="-1" label="number of tags to generate" help="(-tag_count)"/>
    <param name="param_no_tmp_dbs" type="boolean" truevalue="-no_tmp_dbs true" falsevalue="-no_tmp_dbs false" checked="false" optional="True" label="no temporary databases are used" help="(-no_tmp_dbs)"/>
    <param name="param_p_value" type="float" value="1.0" label="annotations with inferior p-value are ignored" help="(-p_value)"/>
    <param name="param_contact_name" type="text" size="20" value="unknown" label="Name of the contact" help="(-contact_name)"/>
    <param name="param_contact_institution" type="text" size="20" value="unknown" label="Name of the contact institution" help="(-contact_institution)"/>
    <param name="param_contact_info" type="text" size="20" value="unknown" label="Some information about the contact" help="(-contact_info)"/>
    <param name="param_blind" type="boolean" truevalue="-blind:blind true" falsevalue="-blind:blind false" checked="false" optional="True" label="perform a blind search (allowing arbitrary modification masses),#br#is preceeded by a normal search to gain a smaller database.#br#(in full mode only)" help="(-blind)"/>
    <param name="param_blind_only" type="boolean" truevalue="-blind:blind_only true" falsevalue="-blind:blind_only false" checked="false" optional="True" label="like blind but no prior search is performed to reduce the database size" help="(-blind_only)"/>
    <param name="param_p_value_blind" type="float" value="1.0" label="used for generating the minimized database" help="(-p_value_blind)"/>
    <param name="param_snd_db" type="text" size="20" label="name of the minimized trie database generated when using blind mode." help="(-snd_db)"/>
    <param name="param_max_ptm_size" type="float" value="250.0" label="maximum modification size (in Da) to consider" help="(-max_ptm_size)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="output file in idXML format.#br#Note: In mode 'inspect_in' an Inspect input file is written." format="idXML"/>
    <data name="param_inspect_output" label="name for the output file of Inspect (may only be used in a full run)" format="data"/>
  </outputs>
  <help>**What it does**

Annotates MS/MS spectra using Inspect.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InspectAdapter.html

@REFERENCES@
</help>
</tool>