Mercurial > repos > galaxyp > openms_fuzzydiff
view FuzzyDiff.xml @ 13:ed9a839cbbda draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author | galaxyp |
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date | Tue, 13 Oct 2020 20:10:05 +0000 |
parents | 36c84cb92e46 |
children | c940abd8d622 |
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<?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 "absdiff" to deal with cases like "zero vs. epsilon""/> <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="<?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> </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/doxygen/release/2.6.0/html/UTILS_FuzzyDiff.html]]></help> <expand macro="references"/> </tool>