annotate InspectAdapter.xml @ 7:1197d1a4c3f6 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5-dirty

<?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: [Identification]-->
<tool id="InspectAdapter" name="InspectAdapter" version="2.3.0">
  <description>Annotates MS/MS spectra using Inspect.</description>
  <macros>
    <token name="@EXECUTABLE@">InspectAdapter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[InspectAdapter

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_inspect_in:
  -inspect_in
#end if
#if $param_inspect_out:
  -inspect_out
#end if
#if $param_inspect_directory:
  -inspect_directory     "$param_inspect_directory"
#end if
#if $param_temp_data_directory:
  -temp_data_directory     "$param_temp_data_directory"
#end if
#if $param_dbs:
  -dbs     "$param_dbs"
#end if
#if $param_trie_dbs:
  -trie_dbs     "$param_trie_dbs"
#end if
#if $param_new_db:
  -new_db     "$param_new_db"
#end if
#if $param_instrument:
  -instrument
  #if " " in str($param_instrument):
    "$param_instrument"
  #else
    $param_instrument
  #end if
#end if
#if $param_precursor_mass_tolerance:
  -precursor_mass_tolerance $param_precursor_mass_tolerance
#end if
#if $param_peak_mass_tolerance:
  -peak_mass_tolerance $param_peak_mass_tolerance
#end if
#if $param_list_modifications:
  -list_modifications
#end if
#if $param_modifications:
  -modifications     "$param_modifications"
#end if
#if $param_use_monoisotopic_mod_mass:
  -use_monoisotopic_mod_mass
#end if
#if $param_modifications_xml_file:
  -modifications_xml_file     "$param_modifications_xml_file"
#end if
#if $param_cleavage:
  -cleavage     "$param_cleavage"
#end if
#if $param_inspect_output:
  -inspect_output $param_inspect_output
#end if
#if $param_inspect_input:
  -inspect_input $param_inspect_input
#end if
#if $param_multicharge:
  -multicharge
#end if
#if $param_max_modifications_pp:
  -max_modifications_pp $param_max_modifications_pp
#end if
#if $param_tag_count:
  -tag_count $param_tag_count
#end if
#if $param_no_tmp_dbs:
  -no_tmp_dbs
#end if
#if $param_p_value:
  -p_value $param_p_value
#end if
#if $param_contact_name:
  -contact_name     "$param_contact_name"
#end if
#if $param_contact_institution:
  -contact_institution     "$param_contact_institution"
#end if
#if $param_contact_info:
  -contact_info     "$param_contact_info"
#end if
#if $param_blind_blind:
  -blind:blind
#end if
#if $param_blind_blind_only:
  -blind:blind_only
#end if
#if $param_blind_p_value_blind:
  -blind:p_value_blind $param_blind_p_value_blind
#end if
#if $param_blind_snd_db:
  -blind:snd_db     "$param_blind_snd_db"
#end if
#if $param_blind_max_ptm_size:
  -blind:max_ptm_size $param_blind_max_ptm_size
#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="mzxml,mzData" optional="False" label="input file in mzXML or mzData format" help="(-in) &lt;br&gt;Note: In mode 'inspect_out' an Inspect results file is read"/>
    <param name="param_inspect_in" display="radio" type="boolean" truevalue="-inspect_in" falsevalue="" checked="false" optional="True" label="if this flag is set the InspectAdapter will read in mzXML, &lt;br&gt;write an Inspect input file and generate a trie database" help="(-inspect_in) "/>
    <param name="param_inspect_out" display="radio" type="boolean" truevalue="-inspect_out" falsevalue="" checked="false" optional="True" label="if this flag is set the InspectAdapter will read in a Inspect results file &lt;br&gt;and write idXML" help="(-inspect_out) "/>
    <param name="param_inspect_directory" type="text" size="30" label="the directory in which Inspect is located" help="(-inspect_directory) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_temp_data_directory" type="text" size="30" label="a directory in which some temporary files can be stored" help="(-temp_data_directory) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_dbs" type="text" size="30" label="name(s) of database(s) to search in (FASTA and SwissProt supported)" help="(-dbs) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_trie_dbs" type="text" size="30" label="name(s) of databases(s) to search in (trie-format)" help="(-trie_dbs) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_new_db" type="text" size="30" label="name of the merged trie database" help="(-new_db) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_instrument" display="radio" type="select" optional="True" label="the instrument that was used to measure the spectra &lt;br&gt;(If set to QTOF, uses a QTOF-derived fragmentation model, &lt;br&gt;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" display="radio" type="boolean" truevalue="-list_modifications" falsevalue="" checked="false" optional="True" label="show a list of the available modifications" help="(-list_modifications) "/>
    <param name="param_modifications" type="text" size="30" label="the colon-separated modifications; may be &lt;br&gt;&lt;name&gt;,&lt;type&gt;," help="(-modifications) e.g.: Deamidation,opt or &lt;br&gt;&lt;composition&gt;,&lt;residues&gt;,&lt;type&gt;,&lt;name&gt;, e.g.: H2C2O,KCS,opt,Acetyl or &lt;br&gt;&lt;mass&gt;,&lt;residues&gt;,&lt;type&gt;,&lt;name&gt;, e.g.: 42.0367,KCS,opt,Acetyl or &lt;br&gt;Valid values for type are &quot;fix&quot; and &quot;opt&quot; (default) &lt;br&gt;If you want terminal PTMs, write &quot;cterm&quot; or &quot;nterm&quot; instead of residues">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_use_monoisotopic_mod_mass" display="radio" type="boolean" truevalue="-use_monoisotopic_mod_mass" falsevalue="" 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="30" label="name of an XML file with the modifications" help="(-modifications_xml_file) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_cleavage" type="text" size="30" value="Trypsin" label="the enzyme used for digestion" help="(-cleavage) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_inspect_input" type="data" format="txt" label="name for the input file of Inspect (may only be used in a full run)" help="(-inspect_input) "/>
    <param name="param_multicharge" display="radio" type="boolean" truevalue="-multicharge" falsevalue="" checked="false" optional="True" label="attempt to guess the precursor charge and mass, &lt;br&gt;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" display="radio" type="boolean" truevalue="-no_tmp_dbs" falsevalue="" 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="30" value="unknown" label="Name of the contact" help="(-contact_name) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_contact_institution" type="text" size="30" value="unknown" label="Name of the contact institution" help="(-contact_institution) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_contact_info" type="text" size="30" value="unknown" label="Some information about the contact" help="(-contact_info) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_blind_blind" display="radio" type="boolean" truevalue="-blind:blind" falsevalue="" checked="false" optional="True" label="perform a blind search (allowing arbitrary modification masses), &lt;br&gt;is preceeded by a normal search to gain a smaller database" help="(-blind) &lt;br&gt;(in full mode only)"/>
    <param name="param_blind_blind_only" display="radio" type="boolean" truevalue="-blind:blind_only" falsevalue="" checked="false" optional="True" label="like blind but no prior search is performed to reduce the database size" help="(-blind_only) "/>
    <param name="param_blind_p_value_blind" type="float" value="1.0" label="used for generating the minimized database" help="(-p_value_blind) "/>
    <param name="param_blind_snd_db" type="text" size="30" label="name of the minimized trie database generated when using blind mode" help="(-snd_db) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_blind_max_ptm_size" type="float" value="250.0" label="maximum modification size (in Da) to conside" help="(-max_ptm_size) "/>
    <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" format="idxml"/>
    <data name="param_inspect_output" format="data"/>
  </outputs>
  <help>Annotates MS/MS spectra using Inspect.


For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_InspectAdapter.html</help>
</tool>