view AdditiveSeries.xml @ 3:75537a09e9fa draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="AdditiveSeries" name="AdditiveSeries" version="2.0.0">
  <description>Computes an additive series to quantify a peptide in a set of samples.</description>
  <macros>
    <token name="@EXECUTABLE@">AdditiveSeries</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>AdditiveSeries

-in
  #for token in $param_in:
    $token
  #end for
#if $param_out:
  -out $param_out
#end if
#if $param_mz_tolerance:
  -mz_tolerance $param_mz_tolerance
#end if
#if $param_rt_tolerance:
  -rt_tolerance $param_rt_tolerance
#end if

#if $rep_param_concentrations:
-concentrations
  #for token in $rep_param_concentrations:
    #if " " in str(token):
      "$token.param_concentrations"
    #else
      $token.param_concentrations
    #end if
  #end for
#end if
#if $param_feature_rt:
  -feature_rt $param_feature_rt
#end if
#if $param_feature_mz:
  -feature_mz $param_feature_mz
#end if
#if $param_standard_rt:
  -standard_rt $param_standard_rt
#end if
#if $param_standard_mz:
  -standard_mz $param_standard_mz
#end if
-threads \${GALAXY_SLOTS:-24} 
#if $param_plot_write_gnuplot_output:
  -plot:write_gnuplot_output
#end if
#if $param_plot_out_gp:
  -plot:out_gp     "$param_plot_out_gp"
#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" multiple="true" optional="False" size="30" label="input files separated by blanks" help="(-in) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_mz_tolerance" type="float" value="1.0" label="Tolerance in m/z dimension" help="(-mz_tolerance) "/>
    <param name="param_rt_tolerance" type="float" value="1.0" label="Tolerance in RT dimension" help="(-rt_tolerance) "/>
    <repeat name="rep_param_concentrations" min="1" title="param_concentrations">
      <param name="param_concentrations" type="text" size="30" value="0" label="List of spiked concentrations" help="(-concentrations) ">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <param name="param_feature_rt" type="float" value="-1.0" label="RT position of the feature" help="(-feature_rt) "/>
    <param name="param_feature_mz" type="float" value="-1.0" label="m/z position of the feature" help="(-feature_mz) "/>
    <param name="param_standard_rt" type="float" value="-1.0" label="RT position of the standard" help="(-standard_rt) "/>
    <param name="param_standard_mz" type="float" value="-1.0" label="m/z position of the standard" help="(-standard_mz) "/>
    <param name="param_plot_write_gnuplot_output" type="boolean" truevalue="-plot:write_gnuplot_output" falsevalue="" checked="false" optional="True" label="Flag that activates the GNUplot output" help="(-write_gnuplot_output) "/>
    <param name="param_plot_out_gp" type="text" size="30" label="base file name (3 files with different extensions are created)" help="(-out_gp) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <expand macro="advanced_options">
      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="xml"/>
  </outputs>
  <help>**What it does**

Computes an additive series to quantify a peptide in a set of samples.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_AdditiveSeries.html</help>
  <expand macro="references"/>
</tool>