Mercurial > repos > galaxyp > openms_peakpickeriterative
diff PeakPickerIterative.xml @ 13:9547baeca6a1 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 18:59:31 +0000 |
| parents | 0c37d0660a6b |
| children | 025261d4bd60 |
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--- a/PeakPickerIterative.xml Fri Nov 06 20:14:18 2020 +0000 +++ b/PeakPickerIterative.xml Thu Dec 01 18:59:31 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: [Signal processing and preprocessing]--> -<tool id="PeakPickerIterative" name="PeakPickerIterative" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="PeakPickerIterative" name="PeakPickerIterative" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Finds mass spectrometric peaks in profile mass spectra.</description> <macros> <token name="@EXECUTABLE@">PeakPickerIterative</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -41,7 +39,7 @@ <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 argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> <param name="signal_to_noise_" argument="-algorithm:signal_to_noise_" type="float" optional="true" value="1.0" label="Signal to noise value, each peak is required to be above this value (turn off by setting it to 0.0)" help=""/> <param name="peak_width" argument="-algorithm:peak_width" type="float" optional="true" value="0.0" label="Expected peak width half width in Dalton - peaks will be extended until this half width is reached (even if the intensitity is increasing)" help="In conjunction with check_width_internally it will also be used to remove peaks whose spacing is larger than this value"/> @@ -54,9 +52,9 @@ <param name="clear_meta_data" argument="-algorithm:clear_meta_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Delete meta data about peak width" help=""/> </section> <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 +67,62 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_PeakPickerIterative"/> - <expand macro="manutest_PeakPickerIterative"/> + <tests><!-- UTILS_PeakPickerIterative_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="PeakPickerIterative_1_input.mzML"/> + <output name="out" file="PeakPickerIterative_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <section name="algorithm"> + <param name="signal_to_noise_" value="1.0"/> + <param name="peak_width" value="0.04"/> + <param name="spacing_difference" value="1.5"/> + <param name="sn_bin_count_" value="30"/> + <param name="nr_iterations_" value="5"/> + <param name="sn_win_len_" value="20.0"/> + <param name="check_width_internally" value="false"/> + <param name="ms1_only" value="false"/> + <param name="clear_meta_data" 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> + </test> + <!-- UTILS_PeakPickerIterative_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="PeakPickerIterative_2_input.mzML"/> + <output name="out" file="PeakPickerIterative_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <section name="algorithm"> + <param name="signal_to_noise_" value="0.0"/> + <param name="peak_width" value="0.04"/> + <param name="spacing_difference" value="2.5"/> + <param name="sn_bin_count_" value="30"/> + <param name="nr_iterations_" value="5"/> + <param name="sn_win_len_" value="20.0"/> + <param name="check_width_internally" value="true"/> + <param name="ms1_only" value="false"/> + <param name="clear_meta_data" 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> + </test> </tests> <help><![CDATA[Finds mass spectrometric peaks in profile mass spectra. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_PeakPickerIterative.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_PeakPickerIterative.html]]></help> <expand macro="references"/> </tool>