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comparison FuzzyDiff.xml @ 15:c940abd8d622 draft

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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 5369624840b9
comparison
equal deleted inserted replaced
14:d98117e7b3b2 15:c940abd8d622
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="FuzzyDiff" name="FuzzyDiff" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="FuzzyDiff" name="FuzzyDiff" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Compares two files, tolerating numeric differences.</description> 5 <description>Compares two files, tolerating numeric differences.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FuzzyDiff</token> 7 <token name="@EXECUTABLE@">FuzzyDiff</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
40 <configfiles> 38 <configfiles>
41 <inputs name="args_json" data_style="paths"/> 39 <inputs name="args_json" data_style="paths"/>
42 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 40 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
43 </configfiles> 41 </configfiles>
44 <inputs> 42 <inputs>
45 <param name="in1" argument="-in1" type="data" format="txt" optional="false" label="first input file" help=" select txt data sets(s)"/> 43 <param argument="-in1" type="data" format="txt" optional="false" label="first input file" help=" select txt data sets(s)"/>
46 <param name="in2" argument="-in2" type="data" format="txt" optional="false" label="second input file" help=" select txt data sets(s)"/> 44 <param argument="-in2" type="data" format="txt" optional="false" label="second input file" help=" select txt data sets(s)"/>
47 <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 &quot;absdiff&quot; to deal with cases like &quot;zero vs. epsilon&quot;"/> 45 <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 &quot;absdiff&quot; to deal with cases like &quot;zero vs. epsilon&quot;"/>
48 <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. "/> 46 <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. "/>
49 <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. "/> 47 <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. "/>
50 <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=""/> 48 <param argument="-tab_width" type="integer" optional="true" min="1" value="8" label="tabulator width, used for calculation of column numbers" help=""/>
51 <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=""/> 49 <param argument="-first_column" type="integer" optional="true" min="0" value="1" label="number of first column, used for calculation of column numbers" help=""/>
52 <expand macro="adv_opts_macro"> 50 <expand macro="adv_opts_macro">
53 <param name="whitelist" argument="-whitelist" type="text" optional="true" value="&lt;?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)"> 51 <param argument="-whitelist" type="text" optional="true" value="&lt;?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)">
54 <expand macro="list_string_val"/> 52 <expand macro="list_string_val" name="whitelist"/>
55 <expand macro="list_string_san"/> 53 <expand macro="list_string_san" name="whitelist"/>
56 </param> 54 </param>
57 <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)"> 55 <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)">
58 <expand macro="list_string_val"/> 56 <expand macro="list_string_val" name="matched_whitelist"/>
59 <expand macro="list_string_san"/> 57 <expand macro="list_string_san" name="matched_whitelist"/>
60 </param> 58 </param>
61 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 59 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
62 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 60 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
63 <expand macro="list_string_san"/> 61 <expand macro="list_string_san" name="test"/>
64 </param> 62 </param>
65 </expand> 63 </expand>
66 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 64 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
67 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 65 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
68 </param> 66 </param>
73 </data> 71 </data>
74 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 72 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
75 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 73 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
76 </data> 74 </data>
77 </outputs> 75 </outputs>
78 <tests> 76 <tests><!-- UTILS_FuzzyDiff_3 -->
79 <expand macro="autotest_FuzzyDiff"/> 77 <test expect_num_outputs="1">
80 <expand macro="manutest_FuzzyDiff"/> 78 <section name="adv_opts">
79 <param name="whitelist" value="&quot;&lt;?xml-stylesheet&quot;"/>
80 <param name="matched_whitelist" value=""/>
81 <param name="force" value="false"/>
82 <param name="test" value="true"/>
83 </section>
84 <param name="in1" value="FuzzyDiff_3_in1.featureXML"/>
85 <param name="in2" value="FuzzyDiff_3_in2.featureXML"/>
86 <param name="ratio" value="1.01"/>
87 <param name="absdiff" value="0.01"/>
88 <param name="verbose" value="1"/>
89 <param name="tab_width" value="8"/>
90 <param name="first_column" value="1"/>
91 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
92 <output name="ctd_out" ftype="xml">
93 <assert_contents>
94 <is_valid_xml/>
95 </assert_contents>
96 </output>
97 </test>
81 </tests> 98 </tests>
82 <help><![CDATA[Compares two files, tolerating numeric differences. 99 <help><![CDATA[Compares two files, tolerating numeric differences.
83 100
84 101
85 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_FuzzyDiff.html]]></help> 102 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_FuzzyDiff.html]]></help>
86 <expand macro="references"/> 103 <expand macro="references"/>
87 </tool> 104 </tool>