<?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="RNPxl" name="RNPxl" version="2.3.0">
  <description>Tool for RNP cross linking experiment analysis.</description>
  <macros>
    <token name="@EXECUTABLE@">RNPxl</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>RNPxl

#if $param_in_mzML:
  -in_mzML $param_in_mzML
#end if
#if $param_length:
  -length $param_length
#end if
#if $param_sequence:
  -sequence     "$param_sequence"
#end if

#if $rep_param_target_nucleotides:
-target_nucleotides
  #for token in $rep_param_target_nucleotides:
    #if " " in str(token):
      "$token.param_target_nucleotides"
    #else
      $token.param_target_nucleotides
    #end if
  #end for
#end if

#if $rep_param_mapping:
-mapping
  #for token in $rep_param_mapping:
    #if " " in str(token):
      "$token.param_mapping"
    #else
      $token.param_mapping
    #end if
  #end for
#end if

#if $rep_param_restrictions:
-restrictions
  #for token in $rep_param_restrictions:
    #if " " in str(token):
      "$token.param_restrictions"
    #else
      $token.param_restrictions
    #end if
  #end for
#end if

#if $rep_param_modifications:
-modifications
  #for token in $rep_param_modifications:
    #if " " in str(token):
      "$token.param_modifications"
    #else
      $token.param_modifications
    #end if
  #end for
#end if
#if $param_peptide_mass_threshold:
  -peptide_mass_threshold $param_peptide_mass_threshold
#end if
#if $param_precursor_variant_mz_threshold:
  -precursor_variant_mz_threshold $param_precursor_variant_mz_threshold
#end if
#if $param_CysteineAdduct:
  -CysteineAdduct
#end if
#if $param_in_OMSSA_ini:
  -in_OMSSA_ini $param_in_OMSSA_ini
#end if
#if $param_in_fasta:
  -in_fasta $param_in_fasta
#end if
#if $param_marker_ions_tolerance:
  -marker_ions_tolerance $param_marker_ions_tolerance
#end if
#if $param_out_idXML:
  -out_idXML $param_out_idXML
#end if
#if $param_out_csv:
  -out_csv $param_out_csv
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_continue:
  -continue
#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in_mzML" type="data" format="mzml" optional="False" label="Input file" help="(-in_mzML) "/>
    <param name="param_length" type="integer" value="4" label="Oligonucleotide maximum length" help="(-length) "/>
    <param name="param_sequence" type="text" size="30" label="Sequence to restrict the generation of oligonucleotide chains" help="(-sequence) (disabled for empty sequence)">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <repeat name="rep_param_target_nucleotides" min="0" max="1" title="param_target_nucleotides">
      <param name="param_target_nucleotides" type="text" size="30" value="A=C10H14N5O7P C=C9H14N3O8P G=C10H14N5O8P U=C9H13N2O9P" label="format:  target nucleotide=empirical formula of nucleoside monophosphate" help="(-target_nucleotides) e.g. A=C10H14N5O7P, ..., U=C10H14N5O7P, X=C9H13N2O8PS  where X represents e.g. tU  &lt;br&gt; or e.g. Y=C10H14N5O7PS where Y represents tG">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <repeat name="rep_param_mapping" min="0" max="1" title="param_mapping">
      <param name="param_mapping" type="text" size="30" value="A-&gt;A C-&gt;C G-&gt;G U-&gt;U" label="format: source-&gt;target e.g. A-&gt;A, ..., U-&gt;U, U-&gt;X" help="(-mapping) ">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <repeat name="rep_param_restrictions" min="0" max="1" title="param_restrictions">
      <param name="param_restrictions" type="text" size="30" value="A=0 C=0 U=0 G=0" label="format: target nucleotide=min_count: e.g U=1 if at least one U must be in the generated sequence" help="(-restrictions) ">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <repeat name="rep_param_modifications" min="0" max="1" title="param_modifications">
      <param name="param_modifications" type="text" size="30" value="-H2O  -H2O-HPO3 -HPO3 -H2O+HPO3 +HPO3" label="format: empirical formula e.g -H2O, ..., H2O+PO3" help="(-modifications) ">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <param name="param_peptide_mass_threshold" type="float" value="600.0" label="Lower peptide mass (Da) threshold" help="(-peptide_mass_threshold) "/>
    <param name="param_precursor_variant_mz_threshold" type="float" value="260.0" label="Lower m/z (Th) threshold for precursor variant" help="(-precursor_variant_mz_threshold) "/>
    <param name="param_CysteineAdduct" display="radio" type="boolean" truevalue="-CysteineAdduct" falsevalue="" checked="false" optional="True" label="Use this flag if the +152 adduct is expected" help="(-CysteineAdduct) "/>
    <param name="param_in_OMSSA_ini" type="data" format="txt" optional="False" label="Ini file for the OMSSA search engine" help="(-in_OMSSA_ini) "/>
    <param name="param_in_fasta" type="data" format="fasta" optional="False" label="Fasta file for search result annotation" help="(-in_fasta) "/>
    <param name="param_marker_ions_tolerance" type="float" value="0.05" label="mz tolerance used to determine marker ions" help="(-marker_ions_tolerance) "/>
    <expand macro="advanced_options">
      <param name="param_continue" display="radio" type="boolean" truevalue="-continue" falsevalue="" checked="false" optional="True" label="Do not recreate intermediate files to continue after unexpected crash" help="(-continue) "/>
      <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_idXML" format="idxml"/>
    <data name="param_out_csv" format="tabular"/>
  </outputs>
  <help>Tool for RNP cross linking experiment analysis.


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