Mercurial > repos > galaxyp > openms_fuzzydiff
diff FuzzyDiff.xml @ 11:36c84cb92e46 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
| author | galaxyp |
|---|---|
| date | Thu, 27 Aug 2020 19:54:16 -0400 |
| parents | 42b3646bc300 |
| children | ed9a839cbbda |
line wrap: on
line diff
--- a/FuzzyDiff.xml Fri May 17 09:24:59 2019 -0400 +++ b/FuzzyDiff.xml Thu Aug 27 19:54:16 2020 -0400 @@ -1,104 +1,87 @@ <?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="2.3.0"> +<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="references"/> + <expand macro="requirements"/> <expand macro="stdio"/> - <expand macro="requirements"/> - <command detect_errors="aggressive"><![CDATA[FuzzyDiff + <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' -#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 -> $param_stdout -]]></command> +## 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="param_in1" type="data" format="txt" label="first input file" help="(-in1) "/> - <param name="param_in2" type="data" format="txt" 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 "absdiff" to deal with cases like "zero vs. epsilon""/> - <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: <br>0 = very quiet mode (absolutely no output) <br>1 = quiet mode (no output unless differences detected) <br>2 = default (include summary at end) <br>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="<?xml-stylesheet" label="Lines containing one of these strings are skipped" help="(-whitelist) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </valid> - </sanitizer> - </param> - </repeat> - <repeat name="rep_param_matched_whitelist" min="0" 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="""/> - </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) "/> + <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="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="param_stdout" format="txt" label="Output from stdout"/> + <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> - <help>Compares two files, tolerating numeric differences. + <tests> + <expand macro="autotest_FuzzyDiff"/> + <expand macro="manutest_FuzzyDiff"/> + </tests> + <help><![CDATA[Compares two files, tolerating numeric differences. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_FuzzyDiff.html</help> +For more information, visit http://www.openms.de/documentation/UTILS_FuzzyDiff.html]]></help> + <expand macro="references"/> </tool>