annotate SeedListGenerator.xml @ 8:f6076d07a33a 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: [Quantitation]-->
<tool id="SeedListGenerator" name="SeedListGenerator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Generates seed lists for feature detection</description>
  <macros>
    <token name="@EXECUTABLE@">SeedListGenerator</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_prefix &&

## 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_prefix
out_prefix/

## Postprocessing
#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="consensusxml,featurexml,idxml,mzml" label="Input file (see below for details)" help=" select consensusxml,featurexml,idxml,mzml data sets(s)"/>
    <param argument="-use_peptide_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)" help=""/>
    <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>
    <collection type="list" name="out_prefix" label="${tool.name} on ${on_string}: out_prefix">
      <discover_datasets directory="out_prefix" recurse="true" format="featurexml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
    </collection>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <!-- TOPP_SeedListGenerator_1 -->
    <!-- TOPP_SeedListGenerator_2 -->
    <!-- TOPP_SeedListGenerator_3 -->
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="test" value="true"/>
      </section>
      <param name="in" value="PepXMLFile_test.mzML"/>
      <output_collection name="out_prefix" count="1">
        <element name="0" file="SeedListGenerator_1_output_tmp_0.featureXML" ftype="featurexml"/>
      </output_collection>
      <param name="use_peptide_mass" value="false"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="test" value="true"/>
      </section>
      <param name="in" value="IDMapper_1_output.featureXML"/>
      <output_collection name="out_prefix" count="1">
        <element name="0" file="SeedListGenerator_2_output_tmp_0.featureXML" ftype="featurexml"/>
      </output_collection>
      <param name="use_peptide_mass" value="false"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <test expect_num_outputs="2">
      <section name="adv_opts">
        <param name="test" value="true"/>
      </section>
      <param name="in" value="ConsensusXMLFile_1.consensusXML"/>
      <output_collection name="out_prefix" count="2">
        <element name="0" file="SeedListGenerator_3_output_tmp_0.featureXML" ftype="featurexml"/>
        <element name="1" file="SeedListGenerator_3_output_tmp_1.featureXML" ftype="featurexml"/>
      </output_collection>
      <param name="use_peptide_mass" value="false"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Generates seed lists for feature detection.


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