annotate FeatureLinkerLabeled.xml @ 16:90a5563d9a69 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906

<!--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: [Feature Linking]-->
<tool id="FeatureLinkerLabeled" name="FeatureLinkerLabeled" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Groups corresponding isotope-labeled features in a feature map</description>
  <macros>
    <token name="@EXECUTABLE@">FeatureLinkerLabeled</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 &&
cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
mkdir out &&

## 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($in.ext)'
-out
'out/output.${gxy2omsext("consensusxml")}'

## Postprocessing
&& mv 'out/output.${gxy2omsext("consensusxml")}' '$out'
#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" label="Input file" help=" select featurexml data sets(s)"/>
    <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
      <param name="rt_estimate" argument="-algorithm:rt_estimate" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance" help="Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance"/>
      <param name="rt_pair_dist" argument="-algorithm:rt_pair_dist" type="float" value="-20.0" label="optimal pair distance in RT [sec] from light to heavy feature" help=""/>
      <param name="rt_dev_low" argument="-algorithm:rt_dev_low" type="float" min="0.0" value="15.0" label="maximum allowed deviation below optimal retention time distance" help=""/>
      <param name="rt_dev_high" argument="-algorithm:rt_dev_high" type="float" min="0.0" value="15.0" label="maximum allowed deviation above optimal retention time distance" help=""/>
      <param name="mz_pair_dists" argument="-algorithm:mz_pair_dists" type="text" value="4.0" label="optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3" help="by division through charge) (space separated list, in order to allow for spaces in list items surround them by single quotes)">
        <expand macro="list_float_valsan" name="mz_pair_dists"/>
      </param>
      <param name="mz_dev" argument="-algorithm:mz_dev" type="float" min="0.0" value="0.05" label="maximum allowed deviation from optimal m/z distance" help=""/>
      <param name="mrm" argument="-algorithm:mrm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)" help=""/>
    </section>
    <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" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
        <expand macro="list_string_san" name="test"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <!-- TOPP_FeatureLinkerLabeled_1 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FeatureLinkerLabeled_1_input.featureXML"/>
      <output name="out" value="FeatureLinkerLabeled_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
      <section name="algorithm">
        <param name="rt_estimate" value="false"/>
        <param name="rt_pair_dist" value="-1.0"/>
        <param name="rt_dev_low" value="0.4"/>
        <param name="rt_dev_high" value="0.4"/>
        <param name="mz_pair_dists" value="8.0"/>
        <param name="mz_dev" value="0.1"/>
        <param name="mrm" value="false"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
    <!-- TOPP_FeatureLinkerLabeled_2 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in" value="FeatureLinkerLabeled_2_input.featureXML"/>
      <output name="out" value="FeatureLinkerLabeled_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
      <section name="algorithm">
        <param name="rt_estimate" value="true"/>
        <param name="rt_pair_dist" value="-121.0382"/>
        <param name="rt_dev_low" value="123.3965"/>
        <param name="rt_dev_high" value="123.3965"/>
        <param name="mz_pair_dists" value="4.0"/>
        <param name="mz_dev" value="0.1"/>
        <param name="mrm" value="false"/>
      </section>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
      <assert_stdout>
        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
      </assert_stdout>
    </test>
  </tests>
  <help><![CDATA[Groups corresponding isotope-labeled features in a feature map.


For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FeatureLinkerLabeled.html]]></help>
  <expand macro="references"/>
</tool>