Mercurial > repos > galaxyp > openms_rnpxlxicfilter
view RNPxlXICFilter.xml @ 8:8a2e37503e3e draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author | galaxyp |
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date | Thu, 27 Aug 2020 19:48:37 -0400 |
parents | 397b489a4f8d |
children | c2827f0ca312 |
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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="RNPxlXICFilter" name="RNPxlXICFilter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Remove MS2 spectra from treatment based on the fold change between control and treatment.</description> <macros> <token name="@EXECUTABLE@">RNPxlXICFilter</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 control && ln -s '$control' 'control/${re.sub("[^\w\-_]", "_", $control.element_identifier)}.$gxy2omsext($control.ext)' && mkdir treatment && ln -s '$treatment' 'treatment/${re.sub("[^\w\-_]", "_", $treatment.element_identifier)}.$gxy2omsext($treatment.ext)' && mkdir out && ## Main program call set -o pipefail && @EXECUTABLE@ -write_ctd ./ && python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && @EXECUTABLE@ -ini @EXECUTABLE@.ctd -control 'control/${re.sub("[^\w\-_]", "_", $control.element_identifier)}.$gxy2omsext($control.ext)' -treatment 'treatment/${re.sub("[^\w\-_]", "_", $treatment.element_identifier)}.$gxy2omsext($treatment.ext)' -out 'out/output.${gxy2omsext("mzml")}' ## Postprocessing && mv 'out/output.${gxy2omsext("mzml")}' '$out' #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="control" argument="-control" type="data" format="mzml" optional="false" label="input mzML file" help=" select mzml data sets(s)"/> <param name="treatment" argument="-treatment" type="data" format="mzml" optional="false" label="input mzML file" help=" select mzml data sets(s)"/> <param name="fold_change" argument="-fold_change" type="float" optional="true" value="2.0" label="fold change between XICs" help=""/> <param name="rt_tol" argument="-rt_tol" type="float" optional="true" value="20.0" 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=""/> <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> </inputs> <outputs> <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> <data name="ctd_out" format="xml" label="${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_RNPxlXICFilter"/> <expand macro="manutest_RNPxlXICFilter"/> </tests> <help><![CDATA[Remove MS2 spectra from treatment based on the fold change between control and treatment. For more information, visit http://www.openms.de/documentation/UTILS_RNPxlXICFilter.html]]></help> <expand macro="references"/> </tool>