annotate FFEval.xml @ 15:71b4a047afe5 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3

<?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: [Utilities]-->
<tool id="FFEval" name="FFEval" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Evaluation tool for feature detection algorithms.</description>
  <macros>
    <token name="@EXECUTABLE@">FFEval</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@
#import re

## Preprocessing
mkdir in &&
ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
mkdir truth &&
ln -s '$truth' 'truth/${re.sub("[^\w\-_]", "_", $truth.element_identifier)}.$gxy2omsext($truth.ext)' &&
#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out &&
#end if
#if $abort_reasons:
  mkdir abort_reasons &&
  ln -s '$abort_reasons' 'abort_reasons/${re.sub("[^\w\-_]", "_", $abort_reasons.element_identifier)}.$gxy2omsext($abort_reasons.ext)' &&
#end if
#if "out_roc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  mkdir out_roc &&
#end if

## Main program call

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
@EXECUTABLE@ -ini @EXECUTABLE@.ctd
-in
'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
-truth
'truth/${re.sub("[^\w\-_]", "_", $truth.element_identifier)}.$gxy2omsext($truth.ext)'
#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out
  'out/output.${gxy2omsext("featurexml")}'
#end if
#if $abort_reasons:
  -abort_reasons
  'abort_reasons/${re.sub("[^\w\-_]", "_", $abort_reasons.element_identifier)}.$gxy2omsext($abort_reasons.ext)'
#end if
#if "out_roc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  -out_roc
  'out_roc/output.${gxy2omsext("csv")}'
#end if
#if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
  | tee '$stdout'
#end if

## Postprocessing
#if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out/output.${gxy2omsext("featurexml")}' '$out'
#end if
#if "out_roc_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
  && mv 'out_roc/output.${gxy2omsext("csv")}' '$out_roc'
#end if
#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
  && mv '@EXECUTABLE@.ctd' '$ctd_out'
#end if]]></command>
  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param argument="-in" type="data" format="featurexml" optional="false" label="Feature input file, which contains the data to be tested against the truth file" help=" select featurexml data sets(s)"/>
    <param argument="-truth" type="data" format="featurexml" optional="false" label="Truth feature file that defines what features should be found" help=" select featurexml data sets(s)"/>
    <param argument="-rt_tol" type="float" optional="true" min="0.0" value="0.3" label="Allowed tolerance of RT relative to average feature RT span" help=""/>
    <param argument="-rt_tol_abs" type="float" optional="true" min="-1.0" value="-1.0" label="Allowed absolute tolerance of RT (overwrites 'rt_tol' if set above zero)" help=""/>
    <param argument="-mz_tol" type="float" optional="true" min="0.0" value="0.25" label="Allowed tolerance in m/z (is divided by charge)" help=""/>
    <param argument="-abort_reasons" type="data" format="featurexml" optional="true" label="Feature file containing seeds with abort reasons" help=" select featurexml data sets(s)"/>
    <expand macro="adv_opts_macro">
      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
        <expand macro="list_string_san" name="test"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="out_FLAG">out (Feature output file)</option>
      <option value="out_roc_FLAG">out_roc (If given, a ROC curve file is created (ROC points based on intensity threshold))</option>
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml">
      <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
    <data name="out_roc" label="${tool.name} on ${on_string}: out_roc" format="csv">
      <filter>OPTIONAL_OUTPUTS is not None and "out_roc_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
    <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
      <filter>OPTIONAL_OUTPUTS is None</filter>
    </data>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests><test expect_num_outputs="2"><!-- comparing an arbitarty FeatureFinder output with itself -->
    <param name="adv_opts|test" value="true"/>
    <param name="in" value="FeatureFinderCentroided_1_output.featureXML"/>
    <param name="truth" value="FeatureFinderCentroided_1_output.featureXML"/>
    <param name="OPTIONAL_OUTPUTS" value="out_FLAG,out_roc_FLAG"/>
    <output name="out" value="FFEval.featureXML" compare="sim_size"/>
	<output name="out_roc" value="FFEval_roc.csv" ftype="csv"/>
  </test>
</tests>
  <help><![CDATA[Evaluation tool for feature detection algorithms.


For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_FFEval.html]]></help>
  <expand macro="references"/>
</tool>