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comparison FuzzyDiff.xml @ 11:36c84cb92e46 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 27 Aug 2020 19:54:16 -0400
parents 42b3646bc300
children ed9a839cbbda
comparison
equal deleted inserted replaced
10:9cc4b157e2fb 11:36c84cb92e46
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="2.3.0"> 4 <tool id="FuzzyDiff" name="FuzzyDiff" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[FuzzyDiff 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in1: 18 ## Preprocessing
16 -in1 $param_in1 19 mkdir in1 &&
17 #end if 20 ln -s '$in1' 'in1/${re.sub("[^\w\-_]", "_", $in1.element_identifier)}.$gxy2omsext($in1.ext)' &&
18 #if $param_in2: 21 mkdir in2 &&
19 -in2 $param_in2 22 ln -s '$in2' 'in2/${re.sub("[^\w\-_]", "_", $in2.element_identifier)}.$gxy2omsext($in2.ext)' &&
20 #end if 23
21 #if $param_ratio: 24 ## Main program call
22 -ratio $param_ratio 25
23 #end if 26 set -o pipefail &&
24 #if $param_absdiff: 27 @EXECUTABLE@ -write_ctd ./ &&
25 -absdiff $param_absdiff 28 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
26 #end if 29 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
27 #if $param_verbose: 30 -in1
28 -verbose $param_verbose 31 'in1/${re.sub("[^\w\-_]", "_", $in1.element_identifier)}.$gxy2omsext($in1.ext)'
29 #end if 32 -in2
30 #if $param_tab_width: 33 'in2/${re.sub("[^\w\-_]", "_", $in2.element_identifier)}.$gxy2omsext($in2.ext)'
31 -tab_width $param_tab_width 34 | tee '$stdout'
32 #end if 35
33 #if $param_first_column: 36 ## Postprocessing
34 -first_column $param_first_column 37 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
35 #end if 38 && mv '@EXECUTABLE@.ctd' '$ctd_out'
36 #if $adv_opts.adv_opts_selector=='advanced': 39 #end if]]></command>
37 40 <configfiles>
38 #if $rep_param_whitelist: 41 <inputs name="args_json" data_style="paths"/>
39 -whitelist 42 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
40 #for token in $rep_param_whitelist: 43 </configfiles>
41 #if " " in str(token):
42 "$token.param_whitelist"
43 #else
44 $token.param_whitelist
45 #end if
46 #end for
47 #end if
48
49 #if $rep_param_matched_whitelist:
50 -matched_whitelist
51 #for token in $rep_param_matched_whitelist:
52 #if " " in str(token):
53 "$token.param_matched_whitelist"
54 #else
55 $token.param_matched_whitelist
56 #end if
57 #end for
58 #end if
59 #if $adv_opts.param_force:
60 -force
61 #end if
62 #end if
63 &gt; $param_stdout
64 ]]></command>
65 <inputs> 44 <inputs>
66 <param name="param_in1" type="data" format="txt" label="first input file" help="(-in1) "/> 45 <param name="in1" argument="-in1" type="data" format="txt" optional="false" label="first input file" help=" select txt data sets(s)"/>
67 <param name="param_in2" type="data" format="txt" label="second input file" help="(-in2) "/> 46 <param name="in2" argument="-in2" type="data" format="txt" optional="false" label="second input file" help=" select txt data sets(s)"/>
68 <param name="param_ratio" type="float" min="1.0" optional="True" value="1.0" label="acceptable relative erro" help="(-ratio) Only one of 'ratio' or 'absdiff' has to be satisfied. Use &quot;absdiff&quot; to deal with cases like &quot;zero vs. epsilon&quot;"/> 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;"/>
69 <param name="param_absdiff" type="float" min="0.0" optional="True" value="0.0" label="acceptable absolute difference" help="(-absdiff) Only one of 'ratio' or 'absdiff' has to be satisfied. "/> 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. "/>
70 <param name="param_verbose" type="integer" min="0" max="3" optional="True" value="2" label="set verbose level: &lt;br&gt;0 = very quiet mode (absolutely no output) &lt;br&gt;1 = quiet mode (no output unless differences detected) &lt;br&gt;2 = default (include summary at end) &lt;br&gt;3 = continue after errors" help="(-verbose) "/> 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. "/>
71 <param name="param_tab_width" type="integer" min="1" optional="True" value="8" label="tabulator width, used for calculation of column numbers" help="(-tab_width) "/> 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=""/>
72 <param name="param_first_column" type="integer" min="0" optional="True" value="1" label="number of first column, used for calculation of column numbers" help="(-first_column) "/> 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=""/>
73 <expand macro="advanced_options"> 52 <expand macro="adv_opts_macro">
74 <repeat name="rep_param_whitelist" min="0" max="1" title="param_whitelist"> 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)">
75 <param name="param_whitelist" type="text" size="30" value="&lt;?xml-stylesheet" label="Lines containing one of these strings are skipped" help="(-whitelist) "> 54 <expand macro="list_string_val"/>
76 <sanitizer> 55 <expand macro="list_string_san"/>
77 <valid initial="string.printable"> 56 </param>
78 <remove value="'"/> 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)">
79 <remove value="&quot;"/> 58 <expand macro="list_string_val"/>
80 </valid> 59 <expand macro="list_string_san"/>
81 </sanitizer> 60 </param>
82 </param> 61 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
83 </repeat> 62 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
84 <repeat name="rep_param_matched_whitelist" min="0" title="param_matched_whitelist"> 63 <expand macro="list_string_san"/>
85 <param name="param_matched_whitelist" type="text" size="30" label="Lines where one file contains one string and the other file another string are skipped. Input is given as list of colon separated tuples," help="(-matched_whitelist) e.g. String1:String2 String3:String4"> 64 </param>
86 <sanitizer>
87 <valid initial="string.printable">
88 <remove value="'"/>
89 <remove value="&quot;"/>
90 </valid>
91 </sanitizer>
92 </param>
93 </repeat>
94 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
95 </expand> 65 </expand>
66 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
67 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
68 </param>
96 </inputs> 69 </inputs>
97 <outputs> 70 <outputs>
98 <data name="param_stdout" format="txt" label="Output from stdout"/> 71 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
72 <filter>OPTIONAL_OUTPUTS is None</filter>
73 </data>
74 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
75 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
76 </data>
99 </outputs> 77 </outputs>
100 <help>Compares two files, tolerating numeric differences. 78 <tests>
79 <expand macro="autotest_FuzzyDiff"/>
80 <expand macro="manutest_FuzzyDiff"/>
81 </tests>
82 <help><![CDATA[Compares two files, tolerating numeric differences.
101 83
102 84
103 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_FuzzyDiff.html</help> 85 For more information, visit http://www.openms.de/documentation/UTILS_FuzzyDiff.html]]></help>
86 <expand macro="references"/>
104 </tool> 87 </tool>