Mercurial > repos > galaxyp > openms_fuzzydiff
comparison FuzzyDiff.xml @ 0:d309f10848f8 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
| author | galaxyp |
|---|---|
| date | Wed, 01 Mar 2017 12:39:44 -0500 |
| parents | |
| children | 2065b42a39e2 |
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| -1:000000000000 | 0:d309f10848f8 |
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| 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 CTD2Galaxy.--> | |
| 3 <!--Proposed Tool Section: [Utilities]--> | |
| 4 <tool id="FuzzyDiff" name="FuzzyDiff" version="2.1.0"> | |
| 5 <description>Compares two files, tolerating numeric differences.</description> | |
| 6 <macros> | |
| 7 <token name="@EXECUTABLE@">FuzzyDiff</token> | |
| 8 <import>macros.xml</import> | |
| 9 </macros> | |
| 10 <expand macro="references"/> | |
| 11 <expand macro="stdio"/> | |
| 12 <expand macro="requirements"/> | |
| 13 <command>FuzzyDiff | |
| 14 | |
| 15 #if $param_in1: | |
| 16 -in1 $param_in1 | |
| 17 #end if | |
| 18 #if $param_in2: | |
| 19 -in2 $param_in2 | |
| 20 #end if | |
| 21 #if $param_ratio: | |
| 22 -ratio $param_ratio | |
| 23 #end if | |
| 24 #if $param_absdiff: | |
| 25 -absdiff $param_absdiff | |
| 26 #end if | |
| 27 #if $param_verbose: | |
| 28 -verbose $param_verbose | |
| 29 #end if | |
| 30 #if $param_tab_width: | |
| 31 -tab_width $param_tab_width | |
| 32 #end if | |
| 33 #if $param_first_column: | |
| 34 -first_column $param_first_column | |
| 35 #end if | |
| 36 #if $adv_opts.adv_opts_selector=='advanced': | |
| 37 | |
| 38 #if $rep_param_whitelist: | |
| 39 -whitelist | |
| 40 #for token in $rep_param_whitelist: | |
| 41 #if " " in str(token): | |
| 42 "$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 > $param_stdout | |
| 64 </command> | |
| 65 <inputs> | |
| 66 <param name="param_in1" type="data" format="text" label="first input file" help="(-in1) "/> | |
| 67 <param name="param_in2" type="data" format="text" label="second input file" help="(-in2) "/> | |
| 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 "absdiff" to deal with cases like "zero vs. epsilon""/> | |
| 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. "/> | |
| 70 <param name="param_verbose" type="integer" min="0" max="3" optional="True" value="2" label="set verbose level: <br>0 = very quiet mode (absolutely no output) <br>1 = quiet mode (no output unless differences detected) <br>2 = default (include summary at end) <br>3 = continue after errors" help="(-verbose) "/> | |
| 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) "/> | |
| 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) "/> | |
| 73 <expand macro="advanced_options"> | |
| 74 <repeat name="rep_param_whitelist" min="0" max="1" title="param_whitelist"> | |
| 75 <param name="param_whitelist" type="text" size="30" value="<?xml-stylesheet" label="Lines containing one of these strings are skipped" help="(-whitelist) "> | |
| 76 <sanitizer> | |
| 77 <valid initial="string.printable"> | |
| 78 <remove value="'"/> | |
| 79 <remove value="""/> | |
| 80 </valid> | |
| 81 </sanitizer> | |
| 82 </param> | |
| 83 </repeat> | |
| 84 <repeat name="rep_param_matched_whitelist" min="0" max="1" title="param_matched_whitelist"> | |
| 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"> | |
| 86 <sanitizer> | |
| 87 <valid initial="string.printable"> | |
| 88 <remove value="'"/> | |
| 89 <remove value="""/> | |
| 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> | |
| 96 </inputs> | |
| 97 <outputs> | |
| 98 <data name="param_stdout" format="text" label="Output from stdout"/> | |
| 99 </outputs> | |
| 100 <help>Compares two files, tolerating numeric differences. | |
| 101 | |
| 102 | |
| 103 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_FuzzyDiff.html</help> | |
| 104 </tool> |