annotate FuzzyDiff.xml @ 2:a09c7f747b9c draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 50c26f7fbe8a2bd1347c860d7a62480865efc254

<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [Utilities]-->
<tool id="FuzzyDiff" name="FuzzyDiff" version="2.1.0">
  <description>Compares two files, tolerating numeric differences.</description>
  <macros>
    <token name="@EXECUTABLE@">FuzzyDiff</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>FuzzyDiff

#if $param_in1:
  -in1 $param_in1
#end if
#if $param_in2:
  -in2 $param_in2
#end if
#if $param_ratio:
  -ratio $param_ratio
#end if
#if $param_absdiff:
  -absdiff $param_absdiff
#end if
#if $param_verbose:
  -verbose $param_verbose
#end if
#if $param_tab_width:
  -tab_width $param_tab_width
#end if
#if $param_first_column:
  -first_column $param_first_column
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    
#if $rep_param_whitelist:
-whitelist
  #for token in $rep_param_whitelist:
    #if " " in str(token):
      "$token.param_whitelist"
    #else
      $token.param_whitelist
    #end if
  #end for
#end if
    
#if $rep_param_matched_whitelist:
-matched_whitelist
  #for token in $rep_param_matched_whitelist:
    #if " " in str(token):
      "$token.param_matched_whitelist"
    #else
      $token.param_matched_whitelist
    #end if
  #end for
#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
&gt; $param_stdout
</command>
  <inputs>
    <param name="param_in1" type="data" format="text" label="first input file" help="(-in1) "/>
    <param name="param_in2" type="data" format="text" label="second input file" help="(-in2) "/>
    <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;"/>
    <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. "/>
    <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) "/>
    <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) "/>
    <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) "/>
    <expand macro="advanced_options">
      <repeat name="rep_param_whitelist" min="0" max="1" title="param_whitelist">
        <param name="param_whitelist" type="text" size="30" value="&lt;?xml-stylesheet" label="Lines containing one of these strings are skipped" help="(-whitelist) ">
          <sanitizer>
            <valid initial="string.printable">
              <remove value="'"/>
              <remove value="&quot;"/>
            </valid>
          </sanitizer>
        </param>
      </repeat>
      <repeat name="rep_param_matched_whitelist" min="0" max="1" title="param_matched_whitelist">
        <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">
          <sanitizer>
            <valid initial="string.printable">
              <remove value="'"/>
              <remove value="&quot;"/>
            </valid>
          </sanitizer>
        </param>
      </repeat>
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_stdout" format="text" label="Output from stdout"/>
  </outputs>
  <help>Compares two files, tolerating numeric differences.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_FuzzyDiff.html</help>
</tool>