Mercurial > repos > galaxyp > openms_idrtcalibration
diff IDRTCalibration.xml @ 15:f7226e34dc70 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
| author | galaxyp |
|---|---|
| date | Fri, 14 Jun 2024 21:38:25 +0000 |
| parents | 7ff821b34ebc |
| children |
line wrap: on
line diff
--- a/IDRTCalibration.xml Thu Dec 01 19:25:24 2022 +0000 +++ b/IDRTCalibration.xml Fri Jun 14 21:38:25 2024 +0000 @@ -1,8 +1,7 @@ -<?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]--> +<!--Proposed Tool Section: [Mass Correction and Calibration]--> <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> + <description>Can be used to calibrate RTs of peptide hits linearly to standards</description> <macros> <token name="@EXECUTABLE@">IDRTCalibration</token> <import>macros.xml</import> @@ -15,7 +14,7 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && ## Main program call @@ -39,14 +38,14 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <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"/> + <param argument="-in" type="data" format="idxml" label="input file" help=" select idxml data sets(s)"/> + <param argument="-calibrant_1_reference" type="float" value="0.1" label="The RT of the first calibrant in the reference file" help=""/> + <param argument="-calibrant_2_reference" type="float" value="0.9" label="The RT of the second calibrant in the reference file" help=""/> + <param argument="-calibrant_1_input" type="float" 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" 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 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=""> + <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> @@ -60,14 +59,15 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- TOPP_IDRTCalibration_1 --> + <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"/> + <output name="out" value="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"/> @@ -78,6 +78,9 @@ <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_IDRTCalibration_2 --> <test expect_num_outputs="2"> @@ -86,7 +89,7 @@ <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"/> + <output name="out" value="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"/> @@ -97,11 +100,14 @@ <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[Can be used to calibrate RTs of peptide hits linearly to standards. -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDRTCalibration.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDRTCalibration.html]]></help> <expand macro="references"/> </tool>