Mercurial > repos > galaxyp > openms_ticcalculator
diff TICCalculator.xml @ 9:32667824b653 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author | galaxyp |
---|---|
date | Thu, 03 Sep 2020 16:16:16 +0000 |
parents | 488ea525e0b1 |
children | ed6c05e730de |
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--- a/TICCalculator.xml Fri May 17 09:56:14 2019 -0400 +++ b/TICCalculator.xml Thu Sep 03 16:16:16 2020 +0000 @@ -1,66 +1,79 @@ <?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="TICCalculator" name="TICCalculator" version="2.3.0"> +<tool id="TICCalculator" name="TICCalculator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).</description> <macros> <token name="@EXECUTABLE@">TICCalculator</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[TICCalculator + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re + +## Preprocessing +mkdir in && +ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && + +## Main program call -#if $param_in: - -in $param_in -#end if -#if $param_read_method: - -read_method - #if " " in str($param_read_method): - "$param_read_method" - #else - $param_read_method - #end if -#end if -#if $param_loadData: - -loadData - #if " " in str($param_loadData): - "$param_loadData" - #else - $param_loadData - #end if -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force -#end if -#end if -> $param_stdout -]]></command> +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && +@EXECUTABLE@ -ini @EXECUTABLE@.ctd +-in +'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' +| tee '$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="param_in" type="data" format="mzData,mzxml,mzml,cachedMzML,dta,dta2d,mgf,featurexml,consensusxml,ms2,fid,tabular,peplist,kroenik,tabular" optional="False" label="Input file to convert" help="(-in) "/> - <param name="param_read_method" type="select" optional="False" value="regular" label="Method to read the file" help="(-read_method) "> + <param name="in" argument="-in" type="data" format="consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular" optional="false" label="Input file to convert" help=" select consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular data sets(s)"/> + <param name="read_method" argument="-read_method" type="select" optional="false" label="Method to read the file" help=""> <option value="regular" selected="true">regular</option> <option value="indexed">indexed</option> <option value="indexed_parallel">indexed_parallel</option> <option value="streaming">streaming</option> <option value="cached">cached</option> <option value="cached_parallel">cached_parallel</option> + <expand macro="list_string_san"/> </param> - <param name="param_loadData" display="radio" type="select" optional="False" value="true" label="Whether to actually load and decode the binary data (or whether to skip decoding the binary data)" help="(-loadData) "> - <option value="true" selected="true">true</option> - <option value="false">false</option> + <param name="loadData" argument="-loadData" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to actually load and decode the binary data (or whether to skip decoding the binary data)" help=""/> + <expand macro="adv_opts_macro"> + <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> - <expand macro="advanced_options"> - <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="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>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking). + <tests> + <expand macro="autotest_TICCalculator"/> + <expand macro="manutest_TICCalculator"/> + </tests> + <help><![CDATA[Calculates the TIC from a mass spectrometric raw file (useful for benchmarking). -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_TICCalculator.html</help> +For more information, visit http://www.openms.de/documentation/UTILS_TICCalculator.html]]></help> + <expand macro="references"/> </tool>