Mercurial > repos > galaxyp > openms_dtaextractor
diff DTAExtractor.xml @ 17:79706b7647c3 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:17:40 +0000 |
| parents | d8b1ec05fbd7 |
| children | 78024781d209 |
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--- a/DTAExtractor.xml Fri Nov 06 20:06:46 2020 +0000 +++ b/DTAExtractor.xml Thu Dec 01 19:17:40 2022 +0000 @@ -1,13 +1,11 @@ <?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@GALAXY_VERSION@" profile="20.05"> +<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> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -38,23 +36,23 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> - <param name="out" 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"/> + <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 name="mz" 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"/> + <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 name="rt" argument="-rt" type="text" optional="true" value=":" label="retention time range of spectra to extract" help=""> - <expand macro="list_string_san"/> + <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 name="level" argument="-level" type="text" optional="true" value="1,2,3" label="MS levels to extract" help=""> - <expand macro="list_string_san"/> + <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 name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> - <expand macro="list_string_san"/> + <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"> @@ -69,13 +67,64 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_DTAExtractor"/> - <expand macro="manutest_DTAExtractor"/> + <tests><!-- TOPP_DTAExtractor_1 --> + <test expect_num_outputs="1"> + <section name="adv_opts"> + <param name="force" value="false"/> + <param name="test" value="true"/> + </section> + <param name="in" value="DTAExtractor_1_input.mzML"/> + <param name="out" value="DTAExtractor"/> + <param name="mz" value=":"/> + <param name="rt" value=":61"/> + <param name="level" value="1,2,3"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <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"/> + <param name="test" value="true"/> + </section> + <param name="in" value="DTAExtractor_1_input.mzML"/> + <param name="out" value="DTAExtractor"/> + <param name="mz" value=":"/> + <param name="rt" value=":"/> + <param name="level" value="1"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <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"/> + <param name="test" value="true"/> + </section> + <param name="in" value="DTAExtractor_1_input.mzML"/> + <param name="out" value="DTAExtractor"/> + <param name="mz" value=":1000"/> + <param name="rt" value=":"/> + <param name="level" value="2"/> + <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[Extracts spectra of an MS run file to several files in DTA format. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_DTAExtractor.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_DTAExtractor.html]]></help> <expand macro="references"/> </tool>