Mercurial > repos > galaxyp > openms_fuzzydiff

annotate FuzzyDiff.xml @ 1:b8b94e9f2cb1 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
author galaxyp
date Tue, 18 Apr 2017 16:06:47 -0400
parents d309f10848f8
children 2065b42a39e2
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d309f10848f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="FuzzyDiff" name="FuzzyDiff" version="2.1.0">
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5 <description>Compares two files, tolerating numeric differences.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FuzzyDiff</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>FuzzyDiff
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14
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15 #if $param_in1:
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16 -in1 $param_in1
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17 #end if
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18 #if $param_in2:
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19 -in2 $param_in2
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20 #end if
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21 #if $param_ratio:
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22 -ratio $param_ratio
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23 #end if
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24 #if $param_absdiff:
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25 -absdiff $param_absdiff
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26 #end if
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27 #if $param_verbose:
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28 -verbose $param_verbose
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29 #end if
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30 #if $param_tab_width:
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31 -tab_width $param_tab_width
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32 #end if
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33 #if $param_first_column:
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34 -first_column $param_first_column
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35 #end if
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36 #if $adv_opts.adv_opts_selector=='advanced':
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37
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38 #if $rep_param_whitelist:
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39 -whitelist
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40 #for token in $rep_param_whitelist:
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41 #if " " in str(token):
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42 "$token.param_whitelist"
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43 #else
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44 $token.param_whitelist
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45 #end if
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46 #end for
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47 #end if
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48
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49 #if $rep_param_matched_whitelist:
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50 -matched_whitelist
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51 #for token in $rep_param_matched_whitelist:
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52 #if " " in str(token):
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53 "$token.param_matched_whitelist"
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54 #else
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55 $token.param_matched_whitelist
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56 #end if
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57 #end for
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58 #end if
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59 #if $adv_opts.param_force:
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60 -force
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61 #end if
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62 #end if
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63 &gt; $param_stdout
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64 </command>
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65 <inputs>
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66 <param name="param_in1" type="data" format="text" label="first input file" help="(-in1) "/>
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67 <param name="param_in2" type="data" format="text" label="second input file" help="(-in2) "/>
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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;"/>
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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. "/>
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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) "/>
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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) "/>
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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) "/>
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73 <expand macro="advanced_options">
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74 <repeat name="rep_param_whitelist" min="0" max="1" title="param_whitelist">
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75 <param name="param_whitelist" type="text" size="30" value="&lt;?xml-stylesheet" label="Lines containing one of these strings are skipped" help="(-whitelist) ">
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76 <sanitizer>
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77 <valid initial="string.printable">
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78 <remove value="'"/>
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79 <remove value="&quot;"/>
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80 </valid>
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81 </sanitizer>
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82 </param>
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83 </repeat>
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84 <repeat name="rep_param_matched_whitelist" min="0" max="1" title="param_matched_whitelist">
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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">
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86 <sanitizer>
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87 <valid initial="string.printable">
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88 <remove value="'"/>
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89 <remove value="&quot;"/>
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90 </valid>
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91 </sanitizer>
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92 </param>
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93 </repeat>
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94 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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95 </expand>
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96 </inputs>
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97 <outputs>
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98 <data name="param_stdout" format="text" label="Output from stdout"/>
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99 </outputs>
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100 <help>Compares two files, tolerating numeric differences.
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101
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102
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103 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_FuzzyDiff.html</help>
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104 </tool>