Mercurial > repos > galaxyp > openms_ticcalculator
diff TICCalculator.xml @ 14:5f36444a0f9d 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 21:43:12 +0000 |
| parents | d623ad21ca59 |
| children |
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--- a/TICCalculator.xml Thu Dec 01 19:10:31 2022 +0000 +++ b/TICCalculator.xml Fri Jun 14 21:43:12 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: [Utilities]--> +<!--Proposed Tool Section: []--> <tool id="TICCalculator" name="TICCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).</description> + <description>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking)</description> <macros> <token name="@EXECUTABLE@">TICCalculator</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)' && ## Main program call @@ -36,8 +35,8 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param argument="-in" type="data" format="consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular" optional="false" label="Input file to convert" help=" select consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular data sets(s)"/> - <param argument="-read_method" type="select" optional="true" label="Method to read the file" help=""> + <param argument="-in" type="data" format="consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular" label="Input file to convert" help=" select consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular data sets(s)"/> + <param argument="-read_method" type="select" label="Method to read the file" help=""> <option value="regular" selected="true">regular</option> <option value="indexed">indexed</option> <option value="indexed_parallel">indexed_parallel</option> @@ -49,7 +48,7 @@ <param argument="-loadData" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to actually load and decode the binary data (or whether to skip decoding the binary data)" help=""/> <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> @@ -65,7 +64,8 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- UTILS_TICCalculator_1 --> + <tests> + <!-- TOPP_TICCalculator_1 --> <test expect_num_outputs="1"> <section name="adv_opts"> <param name="force" value="false"/> @@ -80,8 +80,11 @@ <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> - <!-- UTILS_TICCalculator_2 --> + <!-- TOPP_TICCalculator_2 --> <test expect_num_outputs="1"> <section name="adv_opts"> <param name="force" value="false"/> @@ -96,8 +99,11 @@ <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> - <!-- UTILS_TICCalculator_3 --> + <!-- TOPP_TICCalculator_3 --> <test expect_num_outputs="1"> <section name="adv_opts"> <param name="force" value="false"/> @@ -112,8 +118,11 @@ <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> - <!-- UTILS_TICCalculator_4 --> + <!-- TOPP_TICCalculator_4 --> <test expect_num_outputs="1"> <section name="adv_opts"> <param name="force" value="false"/> @@ -128,8 +137,11 @@ <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> - <!-- UTILS_TICCalculator_5 --> + <!-- TOPP_TICCalculator_5 --> <test expect_num_outputs="1"> <section name="adv_opts"> <param name="force" value="false"/> @@ -144,11 +156,14 @@ <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[Calculates the TIC from a mass spectrometric raw file (useful for benchmarking). -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_TICCalculator.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_TICCalculator.html]]></help> <expand macro="references"/> </tool>