comparison DTAExtractor.xml @ 18:78024781d209 draft default tip

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

17:79706b7647c3

<?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: [File Handling]-->
<tool id="DTAExtractor" name="DTAExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Extracts spectra of an MS run file to several files in DTA format.</description>
  <macros>
    <token name="@EXECUTABLE@">DTAExtractor</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)' &&

## Main program call

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&

  <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="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
    <param argument="-out" type="text" optional="false" value="" label="base name of DTA output files (RT, m/z and extension are appended)" help="">
      <expand macro="list_string_san" name="out"/>
    </param>
    <param argument="-mz" type="text" optional="true" value=":" label="m/z range of precursor peaks to extract" help="This option is ignored for MS level 1">
      <expand macro="list_string_san" name="mz"/>
    </param>
    <param argument="-rt" type="text" optional="true" value=":" label="retention time range of spectra to extract" help="">
      <expand macro="list_string_san" name="rt"/>
    </param>
    <param argument="-level" type="text" optional="true" value="1,2,3" label="MS levels to extract" help="">
      <expand macro="list_string_san" name="level"/>
    </param>
    <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>

    </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><!-- TOPP_DTAExtractor_1 -->
    <test expect_num_outputs="1">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>

      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <!-- TOPP_DTAExtractor_2 -->
    <test expect_num_outputs="1">
      <section name="adv_opts">
        <param name="force" value="false"/>

      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
    <!-- TOPP_DTAExtractor_3 -->
    <test expect_num_outputs="1">
      <section name="adv_opts">
        <param name="force" value="false"/>

      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Extracts spectra of an MS run file to several files in DTA format.


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

18:78024781d209

<!--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: [File Filtering / Extraction / Merging]-->
<tool id="DTAExtractor" name="DTAExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Extracts spectra of an MS run file to several files in DTA format</description>
  <macros>
    <token name="@EXECUTABLE@">DTAExtractor</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)' &&

## Main program call

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&

  <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="mzml" label="input file" help=" select mzml data sets(s)"/>
    <param argument="-out" type="text" value="" label="base name of DTA output files (RT, m/z and extension are appended)" help="">
      <expand macro="list_string_san" name="out"/>
    </param>
    <param argument="-mz" type="text" value=":" label="m/z range of precursor peaks to extract" help="This option is ignored for MS level 1">
      <expand macro="list_string_san" name="mz"/>
    </param>
    <param argument="-rt" type="text" value=":" label="retention time range of spectra to extract" help="">
      <expand macro="list_string_san" name="rt"/>
    </param>
    <param argument="-level" type="text" value="1,2,3" label="MS levels to extract" help="">
      <expand macro="list_string_san" name="level"/>
    </param>
    <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>

    </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>
    <!-- TOPP_DTAExtractor_1 -->
    <test expect_num_outputs="1">
      <section name="adv_opts">
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>

      <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_DTAExtractor_2 -->
    <test expect_num_outputs="1">
      <section name="adv_opts">
        <param name="force" value="false"/>

      <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_DTAExtractor_3 -->
    <test expect_num_outputs="1">
      <section name="adv_opts">
        <param name="force" value="false"/>

      <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[Extracts spectra of an MS run file to several files in DTA format.


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