annotate FuzzyDiff.xml @ 11:36c84cb92e46 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"

<?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@
#import re

## Preprocessing
mkdir in1 &&
ln -s '$in1' 'in1/${re.sub("[^\w\-_]", "_", $in1.element_identifier)}.$gxy2omsext($in1.ext)' &&
mkdir in2 &&
ln -s '$in2' 'in2/${re.sub("[^\w\-_]", "_", $in2.element_identifier)}.$gxy2omsext($in2.ext)' &&

## Main program call

set -o pipefail &&
@EXECUTABLE@ -write_ctd ./ &&
python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
@EXECUTABLE@ -ini @EXECUTABLE@.ctd
-in1
'in1/${re.sub("[^\w\-_]", "_", $in1.element_identifier)}.$gxy2omsext($in1.ext)'
-in2
'in2/${re.sub("[^\w\-_]", "_", $in2.element_identifier)}.$gxy2omsext($in2.ext)'
| tee '$stdout'

## Postprocessing
#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
  && mv '@EXECUTABLE@.ctd' '$ctd_out'
#end if]]></command>
  <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="Overwrite 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" multiple="true" label="Optional outputs" optional="true">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
      <filter>OPTIONAL_OUTPUTS is None</filter>
    </data>
    <data name="ctd_out" format="xml" label="${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/documentation/UTILS_FuzzyDiff.html]]></help>
  <expand macro="references"/>
</tool>