annotate FFEval.xml @ 0:44d9229ac23d draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8

<?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 CTD2Galaxy.-->
<!--Proposed Tool Section: [Utilities]-->
<tool id="FFEval" name="FFEval" version="2.1.0">
  <description>Evaluation tool for feature detection algorithms.</description>
  <macros>
    <token name="@EXECUTABLE@">FFEval</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>FFEval

#if $param_in:
  -in $param_in
#end if
#if $param_truth:
  -truth $param_truth
#end if
#if $param_rt_tol:
  -rt_tol $param_rt_tol
#end if
#if $param_rt_tol_abs:
  -rt_tol_abs $param_rt_tol_abs
#end if
#if $param_mz_tol:
  -mz_tol $param_mz_tol
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_abort_reasons:
  -abort_reasons $param_abort_reasons
#end if
#if $param_out_roc:
  -out_roc $param_out_roc
#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" optional="False" label="Feature input file, which contains the data to be tested against the truth file" help="(-in) "/>
    <param name="param_truth" type="data" format="featurexml" optional="False" label="Truth feature file that defines what features should be found" help="(-truth) "/>
    <param name="param_rt_tol" type="float" min="0.0" optional="True" value="0.3" label="Allowed tolerance of RT relative to average feature RT span" help="(-rt_tol) "/>
    <param name="param_rt_tol_abs" type="float" min="-1.0" optional="True" value="-1.0" label="Allowed absolute tolerance of RT (overwrites 'rt_tol' if set above zero)" help="(-rt_tol_abs) "/>
    <param name="param_mz_tol" type="float" min="0.0" optional="True" value="0.25" label="Allowed tolerance in m/z (is divided by charge)" help="(-mz_tol) "/>
    <param name="param_abort_reasons" type="data" format="featurexml" optional="True" label="Feature file containing seeds with abort reasons" help="(-abort_reasons) "/>
    <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="featurexml"/>
    <data name="param_out_roc" format="tabular"/>
  </outputs>
  <help>Evaluation tool for feature detection algorithms.


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