Mercurial > repos > galaxyp > openms_idrtcalibration
diff IDRTCalibration.xml @ 14:7ff821b34ebc draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
---|---|
date | Thu, 01 Dec 2022 19:25:24 +0000 |
parents | 28805cf9b024 |
children | f7226e34dc70 |
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--- a/IDRTCalibration.xml Fri Nov 06 20:05:16 2020 +0000 +++ b/IDRTCalibration.xml Thu Dec 01 19:25:24 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: [ID Processing]--> -<tool id="IDRTCalibration" name="IDRTCalibration" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="IDRTCalibration" name="IDRTCalibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Can be used to calibrate RTs of peptide hits linearly to standards.</description> <macros> <token name="@EXECUTABLE@">IDRTCalibration</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -41,15 +39,15 @@ <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="calibrant_1_reference" argument="-calibrant_1_reference" type="float" optional="true" value="0.1" label="The RT of the first calibrant in the reference file" help=""/> - <param name="calibrant_2_reference" argument="-calibrant_2_reference" type="float" optional="true" value="0.9" label="The RT of the second calibrant in the reference file" help=""/> - <param name="calibrant_1_input" argument="-calibrant_1_input" type="float" optional="true" value="-1.0" label="The RT of the first calibrant in the input file" help="Please note that this value needs to be set. The default value -1.0 is not allowed"/> - <param name="calibrant_2_input" argument="-calibrant_2_input" type="float" optional="true" value="-1.0" label="The RT of the second calibrant in the input file" help="Please note that this value needs to be set. The default value -1.0 is not allowed"/> + <param argument="-in" type="data" format="idxml" optional="false" label="input file" help=" select idxml data sets(s)"/> + <param argument="-calibrant_1_reference" type="float" optional="true" value="0.1" label="The RT of the first calibrant in the reference file" help=""/> + <param argument="-calibrant_2_reference" type="float" optional="true" value="0.9" label="The RT of the second calibrant in the reference file" help=""/> + <param argument="-calibrant_1_input" type="float" optional="true" value="-1.0" label="The RT of the first calibrant in the input file" help="Please note that this value needs to be set. The default value -1.0 is not allowed"/> + <param argument="-calibrant_2_input" type="float" optional="true" value="-1.0" label="The RT of the second calibrant in the input file" help="Please note that this value needs to be set. The default value -1.0 is not allowed"/> <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"> @@ -62,13 +60,48 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_IDRTCalibration"/> - <expand macro="manutest_IDRTCalibration"/> + <tests><!-- TOPP_IDRTCalibration_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="IDRTCalibration_1_input.idXML"/> + <output name="out" file="IDRTCalibration_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <param name="calibrant_1_reference" value="0.1"/> + <param name="calibrant_2_reference" value="0.9"/> + <param name="calibrant_1_input" value="10.0"/> + <param name="calibrant_2_input" value="90.0"/> + <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> + <output name="ctd_out" ftype="xml"> + <assert_contents> + <is_valid_xml/> + </assert_contents> + </output> + </test> + <!-- TOPP_IDRTCalibration_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="degenerated_empty.idXML"/> + <output name="out" file="IDRTCalibration_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> + <param name="calibrant_1_reference" value="0.1"/> + <param name="calibrant_2_reference" value="0.9"/> + <param name="calibrant_1_input" value="10.0"/> + <param name="calibrant_2_input" value="90.0"/> + <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[Can be used to calibrate RTs of peptide hits linearly to standards. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_IDRTCalibration.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDRTCalibration.html]]></help> <expand macro="references"/> </tool>