comparison FuzzyDiff.xml @ 15:c940abd8d622 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3

14:d98117e7b3b2

<?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 CTDConverter.-->
<!--Proposed Tool Section: [Utilities]-->
<tool id="FuzzyDiff" name="FuzzyDiff" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
  <description>Compares two files, tolerating numeric differences.</description>
  <macros>
    <token name="@EXECUTABLE@">FuzzyDiff</token>
    <import>macros.xml</import>
    <import>macros_autotest.xml</import>
    <import>macros_test.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@

  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param name="in1" argument="-in1" type="data" format="txt" optional="false" label="first input file" help=" select txt data sets(s)"/>
    <param name="in2" argument="-in2" type="data" format="txt" optional="false" label="second input file" help=" select txt data sets(s)"/>
    <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;"/>
    <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. "/>
    <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. "/>
    <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=""/>
    <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=""/>
    <expand macro="adv_opts_macro">
      <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)">
        <expand macro="list_string_val"/>
        <expand macro="list_string_san"/>
      </param>
      <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)">
        <expand macro="list_string_val"/>
        <expand macro="list_string_san"/>
      </param>
      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
        <expand macro="list_string_san"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>

    </data>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <expand macro="autotest_FuzzyDiff"/>
    <expand macro="manutest_FuzzyDiff"/>
  </tests>
  <help><![CDATA[Compares two files, tolerating numeric differences.


For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_FuzzyDiff.html]]></help>
  <expand macro="references"/>
</tool>

15:c940abd8d622

<?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 CTDConverter.-->
<!--Proposed Tool Section: [Utilities]-->
<tool id="FuzzyDiff" name="FuzzyDiff" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
  <description>Compares two files, tolerating numeric differences.</description>
  <macros>
    <token name="@EXECUTABLE@">FuzzyDiff</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@

  <configfiles>
    <inputs name="args_json" data_style="paths"/>
    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
  </configfiles>
  <inputs>
    <param argument="-in1" type="data" format="txt" optional="false" label="first input file" help=" select txt data sets(s)"/>
    <param argument="-in2" type="data" format="txt" optional="false" label="second input file" help=" select txt data sets(s)"/>
    <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;"/>
    <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. "/>
    <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. "/>
    <param argument="-tab_width" type="integer" optional="true" min="1" value="8" label="tabulator width, used for calculation of column numbers" help=""/>
    <param argument="-first_column" type="integer" optional="true" min="0" value="1" label="number of first column, used for calculation of column numbers" help=""/>
    <expand macro="adv_opts_macro">
      <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)">
        <expand macro="list_string_val" name="whitelist"/>
        <expand macro="list_string_san" name="whitelist"/>
      </param>
      <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)">
        <expand macro="list_string_val" name="matched_whitelist"/>
        <expand macro="list_string_san" name="matched_whitelist"/>
      </param>
      <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
        <expand macro="list_string_san" name="test"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>

    </data>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests><!-- UTILS_FuzzyDiff_3 -->
    <test expect_num_outputs="1">
      <section name="adv_opts">
        <param name="whitelist" value="&quot;&lt;?xml-stylesheet&quot;"/>
        <param name="matched_whitelist" value=""/>
        <param name="force" value="false"/>
        <param name="test" value="true"/>
      </section>
      <param name="in1" value="FuzzyDiff_3_in1.featureXML"/>
      <param name="in2" value="FuzzyDiff_3_in2.featureXML"/>
      <param name="ratio" value="1.01"/>
      <param name="absdiff" value="0.01"/>
      <param name="verbose" value="1"/>
      <param name="tab_width" value="8"/>
      <param name="first_column" value="1"/>
      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
      <output name="ctd_out" ftype="xml">
        <assert_contents>
          <is_valid_xml/>
        </assert_contents>
      </output>
    </test>
  </tests>
  <help><![CDATA[Compares two files, tolerating numeric differences.


For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_FuzzyDiff.html]]></help>
  <expand macro="references"/>
</tool>