view AdditiveSeries.xml @ 3:ec62782f6c68 draft

Uploaded

<?xml version='1.0' encoding='UTF-8'?>
<tool id="AdditiveSeries" name="AdditiveSeries" version="1.12.0">
  <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 ${param_in}
-out ${param_out}
-mz_tolerance ${param_mz_tolerance}
-rt_tolerance ${param_rt_tolerance}
-concentrations ${param_concentrations}
-feature_rt ${param_feature_rt}
-feature_mz ${param_feature_mz}
-standard_rt ${param_standard_rt}
-standard_mz ${param_standard_mz}
-threads \${GALAXY_SLOTS:-24} 
${param_write_gnuplot_output}
-plot:out_gp ${param_out_gp}
</command>
  <inputs>
    <param name="param_in" type="data" format="featureXML" optional="False" size="20" label="input files separated by blanks" help="(-in)"/>
    <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)"/>
    <param name="param_concentrations" type="text" size="20" value="0" label="List of spiked concentrations" help="(-concentrations)"/>
    <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_write_gnuplot_output" type="boolean" truevalue="-plot:write_gnuplot_output true" falsevalue="-plot:write_gnuplot_output false" checked="false" optional="True" label="Flag that activates the GNUplot output" help="(-write_gnuplot_output)"/>
    <param name="param_out_gp" type="text" size="20" label="base file name (3 files with different extensions are created)" help="(-out_gp)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="output XML file containg regression line and confidence interval" 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

@REFERENCES@
</help>
</tool>