Mercurial > repos > galaxyp > openms_fuzzydiff
diff FuzzyDiff.xml @ 15:c940abd8d622 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
| author | galaxyp |
|---|---|
| date | Thu, 01 Dec 2022 19:04:01 +0000 |
| parents | ed9a839cbbda |
| children |
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--- a/FuzzyDiff.xml Fri Nov 06 20:32:18 2020 +0000 +++ b/FuzzyDiff.xml Thu Dec 01 19:04:01 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="FuzzyDiff" name="FuzzyDiff" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> +<tool id="FuzzyDiff" name="FuzzyDiff" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Compares two files, tolerating numeric differences.</description> <macros> <token name="@EXECUTABLE@">FuzzyDiff</token> <import>macros.xml</import> - <import>macros_autotest.xml</import> - <import>macros_test.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> @@ -42,25 +40,25 @@ <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param name="in1" argument="-in1" type="data" format="txt" optional="false" label="first input file" help=" select txt data sets(s)"/> - <param name="in2" argument="-in2" type="data" format="txt" optional="false" label="second input file" help=" select txt data sets(s)"/> - <param name="ratio" 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 name="absdiff" 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 name="verbose" 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 name="tab_width" argument="-tab_width" type="integer" optional="true" min="1" value="8" label="tabulator width, used for calculation of column numbers" help=""/> - <param name="first_column" 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" 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=""/> <expand macro="adv_opts_macro"> - <param name="whitelist" 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)"> - <expand macro="list_string_val"/> - <expand macro="list_string_san"/> + <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)"> + <expand macro="list_string_val" name="whitelist"/> + <expand macro="list_string_san" name="whitelist"/> </param> - <param name="matched_whitelist" argument="-matched_whitelist" type="text" optional="true" value="" label="Lines where one file contains one string and the other file another string are skipped" help="Input is given as list of colon separated tuples, e.g. String1:String2 String3:String4 (space separated list, in order to allow for spaces in list items surround them by single quotes)"> - <expand macro="list_string_val"/> - <expand macro="list_string_san"/> + <param argument="-matched_whitelist" type="text" optional="true" value="" label="Lines where one file contains one string and the other file another string are skipped" help="Input is given as list of colon separated tuples, e.g. String1:String2 String3:String4 (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <expand macro="list_string_val" name="matched_whitelist"/> + <expand macro="list_string_san" name="matched_whitelist"/> </param> - <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"> @@ -75,13 +73,32 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests> - <expand macro="autotest_FuzzyDiff"/> - <expand macro="manutest_FuzzyDiff"/> + <tests><!-- UTILS_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> + <param name="in1" value="FuzzyDiff_3_in1.featureXML"/> + <param name="in2" value="FuzzyDiff_3_in2.featureXML"/> + <param name="ratio" value="1.01"/> + <param name="absdiff" value="0.01"/> + <param name="verbose" value="1"/> + <param name="tab_width" value="8"/> + <param name="first_column" value="1"/> + <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[Compares two files, tolerating numeric differences. -For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_FuzzyDiff.html]]></help> +For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_FuzzyDiff.html]]></help> <expand macro="references"/> </tool>