comparison FFEval.xml @ 4:6ead64a594bd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty

3:ec62782f6c68

<?xml version='1.0' encoding='UTF-8'?>
<tool id="FFEval" name="FFEval" version="1.12.0">
  <description>Evaluation tool for feature detection algorithms.</description>
  <macros>
    <token name="@EXECUTABLE@">FFEval</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>FFEval

-in ${param_in}
-truth ${param_truth}
-rt_tol ${param_rt_tol}
-rt_tol_abs ${param_rt_tol_abs}
-mz_tol ${param_mz_tol}
-out ${param_out}
-abort_reasons ${param_abort_reasons}
-out_roc ${param_out_roc}
-threads \${GALAXY_SLOTS:-24} 
</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)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="Feature output file. If given, an annotated input file is written." format="featureXML"/>
    <data name="param_out_roc" label="If given, a ROC curve file is created (ROC points based on intensity threshold)" format="tabular"/>
  </outputs>
  <help>**What it does**

Evaluation tool for feature detection algorithms.


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

@REFERENCES@
</help>
</tool>

4:6ead64a594bd

<?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="2.0.0">
    <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
-threads \${GALAXY_SLOTS:-24}
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
    <inputs>
      <param format="xml" help="(-in) " label="Feature input file, which contains the data to be tested against the truth file" name="param_in" optional="False" type="data"/>
      <param format="xml" help="(-truth) " label="Truth feature file that defines what features should be found" name="param_truth" optional="False" type="data"/>
      <param help="(-rt_tol) " label="Allowed tolerance of RT relative to average feature RT span" min="0.0" name="param_rt_tol" optional="True" type="float" value="0.3"/>
      <param help="(-rt_tol_abs) " label="Allowed absolute tolerance of RT (overwrites 'rt_tol' if set above zero)" min="-1.0" name="param_rt_tol_abs" optional="True" type="float" value="-1.0"/>
      <param help="(-mz_tol) " label="Allowed tolerance in m/z (is divided by charge)" min="0.0" name="param_mz_tol" optional="True" type="float" value="0.25"/>
      <param format="xml" help="(-abort_reasons) " label="Feature file containing seeds with abort reasons" name="param_abort_reasons" optional="True" type="data"/>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="xml" name="param_out"/>
      <data format="tabular" name="param_out_roc"/>
    </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>