Mercurial > repos > galaxyp > openms_fuzzydiff
diff FuzzyDiff.xml @ 16:5369624840b9 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 21:28:23 +0000 |
| parents | c940abd8d622 |
| children |
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--- a/FuzzyDiff.xml Thu Dec 01 19:04:01 2022 +0000 +++ b/FuzzyDiff.xml Fri Jun 14 21:28:23 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: [[for Developers]]--> <tool id="FuzzyDiff" name="FuzzyDiff" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>Compares two files, tolerating numeric differences.</description> + <description>Compares two files, tolerating numeric differences</description> <macros> <token name="@EXECUTABLE@">FuzzyDiff</token> <import>macros.xml</import> @@ -15,9 +14,9 @@ ## Preprocessing mkdir in1 && -ln -s '$in1' 'in1/${re.sub("[^\w\-_]", "_", $in1.element_identifier)}.$gxy2omsext($in1.ext)' && +cp '$in1' 'in1/${re.sub("[^\w\-_]", "_", $in1.element_identifier)}.$gxy2omsext($in1.ext)' && mkdir in2 && -ln -s '$in2' 'in2/${re.sub("[^\w\-_]", "_", $in2.element_identifier)}.$gxy2omsext($in2.ext)' && +cp '$in2' 'in2/${re.sub("[^\w\-_]", "_", $in2.element_identifier)}.$gxy2omsext($in2.ext)' && ## Main program call @@ -40,15 +39,15 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param argument="-in1" type="data" format="txt" optional="false" label="first input file" help=" select txt data sets(s)"/> - <param argument="-in2" type="data" format="txt" optional="false" label="second input file" help=" select txt data sets(s)"/> - <param argument="-ratio" type="float" optional="true" min="1.0" value="1.0" label="acceptable relative erro" help="Only one of 'ratio' or 'absdiff' has to be satisfied. Use "absdiff" to deal with cases like "zero vs. epsilon""/> - <param argument="-absdiff" type="float" optional="true" min="0.0" value="0.0" label="acceptable absolute difference" help="Only one of 'ratio' or 'absdiff' has to be satisfied. "/> - <param argument="-verbose" type="integer" optional="true" min="0" max="3" value="2" label="set verbose level:" help="0 = very quiet mode (absolutely no output). 1 = quiet mode (no output unless differences detected). 2 = default (include summary at end). 3 = continue after errors. "/> - <param argument="-tab_width" type="integer" optional="true" min="1" value="8" label="tabulator width, used for calculation of column numbers" help=""/> - <param argument="-first_column" type="integer" optional="true" min="0" value="1" label="number of first column, used for calculation of column numbers" help=""/> + <param argument="-in1" type="data" format="txt" label="first input file" help=" select txt data sets(s)"/> + <param argument="-in2" type="data" format="txt" label="second input file" help=" select txt data sets(s)"/> + <param argument="-ratio" type="float" min="1.0" value="1.0" label="acceptable relative erro" help="Only one of 'ratio' or 'absdiff' has to be satisfied. Use "absdiff" to deal with cases like "zero vs. epsilon""/> + <param argument="-absdiff" type="float" min="0.0" value="0.0" label="acceptable absolute difference" help="Only one of 'ratio' or 'absdiff' has to be satisfied. "/> + <param argument="-verbose" type="integer" min="0" max="3" value="2" label="set verbose level:" help="0 = very quiet mode (absolutely no output). 1 = quiet mode (no output unless differences detected). 2 = default (include summary at end). 3 = continue after errors. "/> + <param argument="-tab_width" type="integer" min="1" value="8" label="tabulator width, used for calculation of column numbers" help=""/> + <param argument="-first_column" type="integer" min="0" value="1" label="number of first column, used for calculation of column numbers" help=""/> <expand macro="adv_opts_macro"> - <param argument="-whitelist" type="text" optional="true" value="<?xml-stylesheet" label="Lines containing one of these strings are skipped" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <param argument="-whitelist" type="text" value="<?xml-stylesheet" label="Lines containing one of these strings are skipped" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)"> <expand macro="list_string_val" name="whitelist"/> <expand macro="list_string_san" name="whitelist"/> </param> @@ -57,7 +56,7 @@ <expand macro="list_string_san" name="matched_whitelist"/> </param> <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> @@ -73,11 +72,11 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- UTILS_FuzzyDiff_3 --> + <tests> + <!-- TOPP_FuzzyDiff_3 --> <test expect_num_outputs="1"> <section name="adv_opts"> <param name="whitelist" value=""<?xml-stylesheet""/> - <param name="matched_whitelist" value=""/> <param name="force" value="false"/> <param name="test" value="true"/> </section> @@ -94,11 +93,14 @@ <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[Compares two files, tolerating numeric differences. -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_FuzzyDiff.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FuzzyDiff.html]]></help> <expand macro="references"/> </tool>