Mercurial > repos > galaxyp > openms_idscoreswitcher
diff IDScoreSwitcher.xml @ 13:4204882495f2 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
---|---|
date | Thu, 01 Dec 2022 19:20:22 +0000 |
parents | ec0d05b20eed |
children | 5a56ed4fb4c2 |
line wrap: on
line diff
--- a/IDScoreSwitcher.xml Fri Nov 06 20:23:05 2020 +0000 +++ b/IDScoreSwitcher.xml Thu Dec 01 19:20:22 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: [Utilities]--> -<tool id="IDScoreSwitcher" name="IDScoreSwitcher" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="IDScoreSwitcher" name="IDScoreSwitcher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Switches between different scores of peptide or protein hits in identification data</description> <macros> <token name="@EXECUTABLE@">IDScoreSwitcher</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -41,27 +39,26 @@ <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="idxml" optional="false" label="Input file" help=" select idxml data sets(s)"/> - <param name="proteins" argument="-proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply to protein scores instead of PSM scores" help=""/> - <param name="new_score" argument="-new_score" type="text" optional="true" value="" label="Name of the meta value to use as the new score" help=""> - <expand macro="list_string_san"/> + <param argument="-in" type="data" format="idxml" optional="false" label="Input file" help=" select idxml data sets(s)"/> + <param argument="-proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply to protein scores instead of PSM scores" help=""/> + <param argument="-new_score" type="text" optional="true" value="" label="Name of the meta value to use as the new score" help=""> + <expand macro="list_string_san" name="new_score"/> </param> - <param name="new_score_orientation" argument="-new_score_orientation" display="radio" type="select" optional="true" label="Orientation of the new score (are higher or lower values better?)" help=""> - <option value="">default (nothing chosen)</option> + <param argument="-new_score_orientation" type="select" optional="true" label="Orientation of the new score (are higher or lower values better?)" help=""> <option value="lower_better">lower_better</option> <option value="higher_better">higher_better</option> - <expand macro="list_string_san"/> + <expand macro="list_string_san" name="new_score_orientation"/> </param> - <param name="new_score_type" argument="-new_score_type" type="text" optional="true" value="" label="Name to use as the type of the new score (default: same as 'new_score')" help=""> - <expand macro="list_string_san"/> + <param argument="-new_score_type" type="text" optional="true" value="" label="Name to use as the type of the new score (default: same as 'new_score')" help=""> + <expand macro="list_string_san" name="new_score_type"/> </param> - <param name="old_score" argument="-old_score" type="text" optional="true" value="" label="Name to use for the meta value storing the old score (default: old score type)" help=""> - <expand macro="list_string_san"/> + <param argument="-old_score" type="text" optional="true" value="" label="Name to use for the meta value storing the old score (default: old score type)" help=""> + <expand macro="list_string_san" name="old_score"/> </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"> @@ -74,13 +71,50 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_IDScoreSwitcher"/> - <expand macro="manutest_IDScoreSwitcher"/> + <tests><!-- UTILS_IDScoreSwitcher_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="IDFileConverter_12_output.idXML"/> + <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <param name="proteins" value="false"/> + <param name="new_score" value="Percolator_PEP"/> + <param name="new_score_orientation" value="lower_better"/> + <param name="new_score_type" value="Posterior Error Probability"/> + <param name="old_score" value="Percolator_qvalue"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- UTILS_IDScoreSwitcher_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="IDScoreSwitcher_2_input.idXML"/> + <output name="out" file="IDScoreSwitcher_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <param name="proteins" value="true"/> + <param name="new_score" value="Posterior Probability_score"/> + <param name="new_score_orientation" value="higher_better"/> + <param name="new_score_type" value="Posterior Probability"/> + <param name="old_score" value=""/> + <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[Switches between different scores of peptide or protein hits in identification data -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_IDScoreSwitcher.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_IDScoreSwitcher.html]]></help> <expand macro="references"/> </tool>