comparison SeedListGenerator.xml @ 8:f6076d07a33a draft default tip

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

7:f3c72f54b9eb

<?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: [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"/>

@EXT_FOO@
#import re

## Preprocessing
mkdir in &&
ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
mkdir out_prefix &&

## Main program call

set -o pipefail &&

  <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,idxml,mzml" optional="false" label="Input file (see below for details)" help=" select 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" 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="ctd_out_FLAG">Output used ctd (ini) configuration file</option>

    </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">

      <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">

      <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">

        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
</tests>
  <help><![CDATA[Generates seed lists for feature detection.


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

8:f6076d07a33a

<!--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"/>

@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 &&

  <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>

    </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">

      <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">

      <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">

        <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>