Mercurial > repos > galaxyp > openms_eicextractor
view EICExtractor.xml @ 14:3cedbe742c68 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 2adf8edc3de4e1cd3b299b26abb14544d17d0636"
author | galaxyp |
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date | Fri, 06 Nov 2020 20:20:11 +0000 |
parents | 0546885ddaf9 |
children | f253d41d9170 |
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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: [Quantitation]--> <tool id="EICExtractor" name="EICExtractor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Extracts intensities from dedicates positions in a LC/MS map</description> <macros> <token name="@EXECUTABLE@">EICExtractor</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 in && ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } #if $in_header: mkdir in_header && ${ ' '.join(["ln -s '%s' 'in_header/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_header if _]) } #end if mkdir pos && ln -s '$pos' 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)' && mkdir out && #if "out_debug_TIC_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir auto_rt_out_debug_TIC && #end if ## 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 -in ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} #if $in_header: -in_header ${' '.join(["'in_header/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_header if _])} #end if -pos 'pos/${re.sub("[^\w\-_]", "_", $pos.element_identifier)}.$gxy2omsext($pos.ext)' -out 'out/output.${gxy2omsext("csv")}' #if "out_debug_TIC_FLAG" in str($OPTIONAL_OUTPUTS).split(',') -auto_rt:out_debug_TIC 'auto_rt_out_debug_TIC/output.${gxy2omsext("mzml")}' #end if #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 | tee '$stdout' #end if ## Postprocessing && mv 'out/output.${gxy2omsext("csv")}' '$out' #if "out_debug_TIC_FLAG" in str($OPTIONAL_OUTPUTS).split(',') && mv 'auto_rt_out_debug_TIC/output.${gxy2omsext("mzml")}' '$auto_rt_out_debug_TIC' #end if #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="in" argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input raw data file" help=" select mzml data sets(s)"/> <param name="in_header" argument="-in_header" type="data" format="txt" multiple="true" optional="true" label="[for Waters data only] Read additional information from _HEADER.TXT" help="Provide one for each raw input file select txt data sets(s)"/> <param name="pos" argument="-pos" type="data" format="edta" optional="false" label="Input config file stating where to find signal" help=" select edta data sets(s)"/> <param name="rt_tol" argument="-rt_tol" type="float" optional="true" value="3.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help=""/> <param name="mz_tol" argument="-mz_tol" type="float" optional="true" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help=""/> <param name="rt_collect" argument="-rt_collect" type="integer" optional="true" value="1" label="# of scans up & down in RT from highest point for ppm estimation in result" help=""/> <section name="auto_rt" title="Parameters for automatic detection of injection RT peaks (no need to specify them in 'pos' input file)" help="" expanded="false"> <param name="enabled" argument="-auto_rt:enabled" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Automatically detect injection peaks from TIC and quantify all m/z x RT combinations" help=""/> <param name="FHWM" argument="-auto_rt:FHWM" type="float" optional="true" value="5.0" label="Expected full width at half-maximum of each raw RT peak in [s]" help="Gaussian smoothing filter with this width is applied to TIC"/> <param name="SNThreshold" argument="-auto_rt:SNThreshold" type="float" optional="true" value="5.0" label="S/N threshold for a smoothed raw peak to pass peak picking" help="Higher thesholds will result in less peaks"/> </section> <expand macro="adv_opts_macro"> <param name="out_separator" argument="-out_separator" type="text" optional="true" value="," label="Separator character for output CSV file" help=""> <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="out_debug_TIC_FLAG">out_debug_TIC (Optional output file (for first input) containing the smoothed TIC, S/N levels and picked RT positions)</option> <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> </param> </inputs> <outputs> <data name="out" label="${tool.name} on ${on_string}: out" format="csv"/> <data name="auto_rt_out_debug_TIC" label="${tool.name} on ${on_string}: auto_rt:out_debug_TIC" format="mzml"> <filter>OPTIONAL_OUTPUTS is not None and "out_debug_TIC_FLAG" in OPTIONAL_OUTPUTS</filter> </data> <data name="ctd_out" format="xml" label="${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_EICExtractor"/> <expand macro="manutest_EICExtractor"/> </tests> <help><![CDATA[Extracts intensities from dedicates positions in a LC/MS map For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_EICExtractor.html]]></help> <expand macro="references"/> </tool>