annotate ProteinQuantifier.xml @ 5:fbae1b1acf70 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b

<?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: [Quantitation]-->
<tool id="ProteinQuantifier" name="ProteinQuantifier" version="2.3.0">
  <description>Compute peptide and protein abundances</description>
  <macros>
    <token name="@EXECUTABLE@">ProteinQuantifier</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>ProteinQuantifier

#if $param_in:
  -in $param_in
#end if
#if $param_protein_groups:
  -protein_groups $param_protein_groups
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_peptide_out:
  -peptide_out $param_peptide_out
#end if
#if $param_top:
  -top $param_top
#end if
#if $param_average:
  -average
  #if " " in str($param_average):
    "$param_average"
  #else
    $param_average
  #end if
#end if
#if $param_include_all:
  -include_all
#end if
#if $param_filter_charge:
  -filter_charge
#end if
#if $param_ratios:
  -ratios
#end if
#if $param_ratiosSILAC:
  -ratiosSILAC
#end if
#if $param_consensus_normalize:
  -consensus:normalize
#end if
#if $param_consensus_fix_peptides:
  -consensus:fix_peptides
#end if
#if $param_format_separator:
  -format:separator     "$param_format_separator"
#end if
#if $param_format_quoting:
  -format:quoting
  #if " " in str($param_format_quoting):
    "$param_format_quoting"
  #else
    $param_format_quoting
  #end if
#end if
#if $param_format_replacement:
  -format:replacement     "$param_format_replacement"
#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="featurexml,consensusxml,idxml" optional="False" label="Input file" help="(-in) "/>
    <param name="param_protein_groups" type="data" format="idxml" optional="True" label="Protein inference results for the identification runs that were used to annotate the input (" help="(-protein_groups) e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter). &lt;br&gt;Information about indistinguishable proteins will be used for protein quantification"/>
    <param name="param_top" type="integer" min="0" optional="True" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help="(-top) "/>
    <param name="param_average" display="radio" type="select" optional="False" value="median" label="Averaging method used to compute protein abundances from peptide abundances" help="(-average) ">
      <option value="median" selected="true">median</option>
      <option value="mean">mean</option>
      <option value="weighted_mean">weighted_mean</option>
      <option value="sum">sum</option>
    </param>
    <param name="param_include_all" display="radio" type="boolean" truevalue="-include_all" falsevalue="" checked="false" optional="True" label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" help="(-include_all) "/>
    <param name="param_filter_charge" display="radio" type="boolean" truevalue="-filter_charge" falsevalue="" checked="false" optional="True" label="Distinguish between charge states of a peptide" help="(-filter_charge) For peptides, abundances will be reported separately for each charge; &lt;br&gt;for proteins, abundances will be computed based only on the most prevalent charge of each peptide. &lt;br&gt;By default, abundances are summed over all charge states"/>
    <param name="param_ratios" display="radio" type="boolean" truevalue="-ratios" falsevalue="" checked="false" optional="True" label="Add the log2 ratios of the abundance values to the output" help="(-ratios) Format: log_2(x_0/x_0) &lt;sep&gt; log_2(x_1/x_0) &lt;sep&gt; log_2(x_2/x_0) "/>
    <param name="param_ratiosSILAC" display="radio" type="boolean" truevalue="-ratiosSILAC" falsevalue="" checked="false" optional="True" label="Add the log2 ratios for a triple SILAC experiment to the output" help="(-ratiosSILAC) Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) &lt;sep&gt; log_2(heavy/middle) &lt;sep&gt; log_2(middle/light)"/>
    <param name="param_consensus_normalize" display="radio" type="boolean" truevalue="-consensus:normalize" falsevalue="" checked="false" optional="True" label="Scale peptide abundances so that medians of all samples are equal" help="(-normalize) "/>
    <param name="param_consensus_fix_peptides" display="radio" type="boolean" truevalue="-consensus:fix_peptides" falsevalue="" checked="false" optional="True" label="Use the same peptides for protein quantification across all samples" help="(-fix_peptides) &lt;br&gt;With 'top 0', all peptides that occur in every sample are considered. &lt;br&gt;Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected, &lt;br&gt;breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)"/>
    <param name="param_format_separator" type="text" size="30" label="Character(s) used to separate fields; by default, the 'tab' character is used" help="(-separator) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_format_quoting" display="radio" type="select" optional="False" value="double" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes, &lt;br&gt;'escape' for quoting with backslash-escaping of embedded quotes" help="(-quoting) ">
      <option value="none">none</option>
      <option value="double" selected="true">double</option>
      <option value="escape">escape</option>
    </param>
    <param name="param_format_replacement" type="text" size="30" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help="(-replacement) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <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="tabular"/>
    <data name="param_peptide_out" format="tabular"/>
  </outputs>
  <help>Compute peptide and protein abundances


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