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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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15:c940abd8d622 16:5369624840b9
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.--> 1 <!--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]--> 2 <!--Proposed Tool Section: [[for Developers]]-->
4 <tool id="FuzzyDiff" name="FuzzyDiff" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="FuzzyDiff" name="FuzzyDiff" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Compares two files, tolerating numeric differences.</description> 4 <description>Compares two files, tolerating numeric differences</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">FuzzyDiff</token> 6 <token name="@EXECUTABLE@">FuzzyDiff</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in1 && 16 mkdir in1 &&
18 ln -s '$in1' 'in1/${re.sub("[^\w\-_]", "_", $in1.element_identifier)}.$gxy2omsext($in1.ext)' && 17 cp '$in1' 'in1/${re.sub("[^\w\-_]", "_", $in1.element_identifier)}.$gxy2omsext($in1.ext)' &&
19 mkdir in2 && 18 mkdir in2 &&
20 ln -s '$in2' 'in2/${re.sub("[^\w\-_]", "_", $in2.element_identifier)}.$gxy2omsext($in2.ext)' && 19 cp '$in2' 'in2/${re.sub("[^\w\-_]", "_", $in2.element_identifier)}.$gxy2omsext($in2.ext)' &&
21 20
22 ## Main program call 21 ## Main program call
23 22
24 set -o pipefail && 23 set -o pipefail &&
25 @EXECUTABLE@ -write_ctd ./ && 24 @EXECUTABLE@ -write_ctd ./ &&
38 <configfiles> 37 <configfiles>
39 <inputs name="args_json" data_style="paths"/> 38 <inputs name="args_json" data_style="paths"/>
40 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
41 </configfiles> 40 </configfiles>
42 <inputs> 41 <inputs>
43 <param argument="-in1" type="data" format="txt" optional="false" label="first input file" help=" select txt data sets(s)"/> 42 <param argument="-in1" type="data" format="txt" label="first 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)"/> 43 <param argument="-in2" type="data" format="txt" label="second input file" help=" select txt data sets(s)"/>
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;"/> 44 <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 &quot;absdiff&quot; to deal with cases like &quot;zero vs. epsilon&quot;"/>
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. "/> 45 <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. "/>
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. "/> 46 <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. "/>
48 <param argument="-tab_width" type="integer" optional="true" min="1" value="8" label="tabulator width, used for calculation of column numbers" help=""/> 47 <param argument="-tab_width" type="integer" min="1" value="8" label="tabulator width, 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=""/> 48 <param argument="-first_column" type="integer" min="0" value="1" label="number of first column, used for calculation of column numbers" help=""/>
50 <expand macro="adv_opts_macro"> 49 <expand macro="adv_opts_macro">
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)"> 50 <param argument="-whitelist" type="text" 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)">
52 <expand macro="list_string_val" name="whitelist"/> 51 <expand macro="list_string_val" name="whitelist"/>
53 <expand macro="list_string_san" name="whitelist"/> 52 <expand macro="list_string_san" name="whitelist"/>
54 </param> 53 </param>
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)"> 54 <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)">
56 <expand macro="list_string_val" name="matched_whitelist"/> 55 <expand macro="list_string_val" name="matched_whitelist"/>
57 <expand macro="list_string_san" name="matched_whitelist"/> 56 <expand macro="list_string_san" name="matched_whitelist"/>
58 </param> 57 </param>
59 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 58 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
60 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 59 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
61 <expand macro="list_string_san" name="test"/> 60 <expand macro="list_string_san" name="test"/>
62 </param> 61 </param>
63 </expand> 62 </expand>
64 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 63 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
65 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 64 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
71 </data> 70 </data>
72 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 71 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
73 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 72 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
74 </data> 73 </data>
75 </outputs> 74 </outputs>
76 <tests><!-- UTILS_FuzzyDiff_3 --> 75 <tests>
76 <!-- TOPP_FuzzyDiff_3 -->
77 <test expect_num_outputs="1"> 77 <test expect_num_outputs="1">
78 <section name="adv_opts"> 78 <section name="adv_opts">
79 <param name="whitelist" value="&quot;&lt;?xml-stylesheet&quot;"/> 79 <param name="whitelist" value="&quot;&lt;?xml-stylesheet&quot;"/>
80 <param name="matched_whitelist" value=""/>
81 <param name="force" value="false"/> 80 <param name="force" value="false"/>
82 <param name="test" value="true"/> 81 <param name="test" value="true"/>
83 </section> 82 </section>
84 <param name="in1" value="FuzzyDiff_3_in1.featureXML"/> 83 <param name="in1" value="FuzzyDiff_3_in1.featureXML"/>
85 <param name="in2" value="FuzzyDiff_3_in2.featureXML"/> 84 <param name="in2" value="FuzzyDiff_3_in2.featureXML"/>
92 <output name="ctd_out" ftype="xml"> 91 <output name="ctd_out" ftype="xml">
93 <assert_contents> 92 <assert_contents>
94 <is_valid_xml/> 93 <is_valid_xml/>
95 </assert_contents> 94 </assert_contents>
96 </output> 95 </output>
96 <assert_stdout>
97 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
98 </assert_stdout>
97 </test> 99 </test>
98 </tests> 100 </tests>
99 <help><![CDATA[Compares two files, tolerating numeric differences. 101 <help><![CDATA[Compares two files, tolerating numeric differences.
100 102
101 103
102 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_FuzzyDiff.html]]></help> 104 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FuzzyDiff.html]]></help>
103 <expand macro="references"/> 105 <expand macro="references"/>
104 </tool> 106 </tool>