annotate MultiplexResolver.xml @ 6:7b9dd0796558 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb

<?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="MultiplexResolver" name="MultiplexResolver" version="2.3.0">
  <description>Completes peptide multiplets and resolves conflicts within them.</description>
  <macros>
    <token name="@EXECUTABLE@">MultiplexResolver</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>MultiplexResolver

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_out_conflicts:
  -out_conflicts $param_out_conflicts
#end if
#if $param_algorithm_labels:
  -algorithm:labels     "$param_algorithm_labels"
#end if
#if $param_algorithm_missed_cleavages:
  -algorithm:missed_cleavages $param_algorithm_missed_cleavages
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_algorithm_mass_tolerance:
  -algorithm:mass_tolerance $adv_opts.param_algorithm_mass_tolerance
#end if
    #if $adv_opts.param_labels_Arg6:
  -labels:Arg6 $adv_opts.param_labels_Arg6
#end if
    #if $adv_opts.param_labels_Arg10:
  -labels:Arg10 $adv_opts.param_labels_Arg10
#end if
    #if $adv_opts.param_labels_Lys4:
  -labels:Lys4 $adv_opts.param_labels_Lys4
#end if
    #if $adv_opts.param_labels_Lys6:
  -labels:Lys6 $adv_opts.param_labels_Lys6
#end if
    #if $adv_opts.param_labels_Lys8:
  -labels:Lys8 $adv_opts.param_labels_Lys8
#end if
    #if $adv_opts.param_labels_Leu3:
  -labels:Leu3 $adv_opts.param_labels_Leu3
#end if
    #if $adv_opts.param_labels_Dimethyl0:
  -labels:Dimethyl0 $adv_opts.param_labels_Dimethyl0
#end if
    #if $adv_opts.param_labels_Dimethyl4:
  -labels:Dimethyl4 $adv_opts.param_labels_Dimethyl4
#end if
    #if $adv_opts.param_labels_Dimethyl6:
  -labels:Dimethyl6 $adv_opts.param_labels_Dimethyl6
#end if
    #if $adv_opts.param_labels_Dimethyl8:
  -labels:Dimethyl8 $adv_opts.param_labels_Dimethyl8
#end if
    #if $adv_opts.param_labels_ICPL0:
  -labels:ICPL0 $adv_opts.param_labels_ICPL0
#end if
    #if $adv_opts.param_labels_ICPL4:
  -labels:ICPL4 $adv_opts.param_labels_ICPL4
#end if
    #if $adv_opts.param_labels_ICPL6:
  -labels:ICPL6 $adv_opts.param_labels_ICPL6
#end if
    #if $adv_opts.param_labels_ICPL10:
  -labels:ICPL10 $adv_opts.param_labels_ICPL10
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="consensusxml" optional="False" label="Peptide multiplets with assigned sequence information" help="(-in) "/>
    <param name="param_algorithm_labels" type="text" size="30" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="(-labels) [...] specifies the labels for a single sample. For example &lt;br&gt; &lt;br&gt;[][Lys8,Arg10]        ... SILAC &lt;br&gt;[][Lys4,Arg6][Lys8,Arg10]        ... triple-SILAC &lt;br&gt;[Dimethyl0][Dimethyl6]        ... Dimethyl &lt;br&gt;[Dimethyl0][Dimethyl4][Dimethyl8]        ... triple Dimethyl &lt;br&gt;[ICPL0][ICPL4][ICPL6][ICPL10]        ... ICPL">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_algorithm_missed_cleavages" type="integer" min="0" optional="True" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(-missed_cleavages) (Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/>
    <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) "/>
      <param name="param_algorithm_mass_tolerance" type="float" value="0.1" label="Mass tolerance in Da for matching the detected to the theoretical mass shifts" help="(-mass_tolerance) "/>
      <param name="param_labels_Arg6" type="float" min="0.0" optional="True" value="6.0201290268" label="Label:13C(6)  |  C(-6) 13C(6)  |  unimod #188" help="(-Arg6) "/>
      <param name="param_labels_Arg10" type="float" min="0.0" optional="True" value="10.0082686" label="Label:13C(6)15N(4)  |  C(-6) 13C(6) N(-4) 15N(4)  |  unimod #267" help="(-Arg10) "/>
      <param name="param_labels_Lys4" type="float" min="0.0" optional="True" value="4.0251069836" label="Label:2H(4)  |  H(-4) 2H(4)  |  unimod #481" help="(-Lys4) "/>
      <param name="param_labels_Lys6" type="float" min="0.0" optional="True" value="6.0201290268" label="Label:13C(6)  |  C(-6) 13C(6)  |  unimod #188" help="(-Lys6) "/>
      <param name="param_labels_Lys8" type="float" min="0.0" optional="True" value="8.0141988132" label="Label:13C(6)15N(2)  |  C(-6) 13C(6) N(-2) 15N(2)  |  unimod #259" help="(-Lys8) "/>
      <param name="param_labels_Leu3" type="float" min="0.0" optional="True" value="3.01883" label="Label:2H(3)  |  H(-3) 2H(3)  |  unimod #262" help="(-Leu3) "/>
      <param name="param_labels_Dimethyl0" type="float" min="0.0" optional="True" value="28.0313" label="Dimethyl  |  H(4) C(2)  |  unimod #36" help="(-Dimethyl0) "/>
      <param name="param_labels_Dimethyl4" type="float" min="0.0" optional="True" value="32.056407" label="Dimethyl:2H(4)  |  2H(4) C(2)  |  unimod #199" help="(-Dimethyl4) "/>
      <param name="param_labels_Dimethyl6" type="float" min="0.0" optional="True" value="34.063117" label="Dimethyl:2H(4)13C(2)  |  2H(4) 13C(2)  |  unimod #510" help="(-Dimethyl6) "/>
      <param name="param_labels_Dimethyl8" type="float" min="0.0" optional="True" value="36.07567" label="Dimethyl:2H(6)13C(2)  |  H(-2) 2H(6) 13C(2)  |  unimod #330" help="(-Dimethyl8) "/>
      <param name="param_labels_ICPL0" type="float" min="0.0" optional="True" value="105.021464" label="ICPL  |  H(3) C(6) N O  |  unimod #365" help="(-ICPL0) "/>
      <param name="param_labels_ICPL4" type="float" min="0.0" optional="True" value="109.046571" label="ICPL:2H(4)  |  H(-1) 2H(4) C(6) N O  |  unimod #687" help="(-ICPL4) "/>
      <param name="param_labels_ICPL6" type="float" min="0.0" optional="True" value="111.041593" label="ICPL:13C(6)  |  H(3) 13C(6) N O  |  unimod #364" help="(-ICPL6) "/>
      <param name="param_labels_ICPL10" type="float" min="0.0" optional="True" value="115.0667" label="ICPL:13C(6)2H(4)  |  H(-1) 2H(4) 13C(6) N O  |  unimod #866" help="(-ICPL10) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="consensusxml"/>
    <data name="param_out_conflicts" format="consensusxml"/>
  </outputs>
  <help>Completes peptide multiplets and resolves conflicts within them.


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