Mercurial > repos > galaxyp > openms_internalcalibration
diff InternalCalibration.xml @ 14:a1dffbb8fbc3 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
| author | galaxyp |
|---|---|
| date | Fri, 14 Jun 2024 21:27:54 +0000 |
| parents | f49a58e03ada |
| children |
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--- a/InternalCalibration.xml Thu Dec 01 19:14:27 2022 +0000 +++ b/InternalCalibration.xml Fri Jun 14 21:27:54 2024 +0000 @@ -1,8 +1,7 @@ -<?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: [Signal processing and preprocessing]--> +<!--Proposed Tool Section: [Mass Correction and Calibration]--> <tool id="InternalCalibration" name="InternalCalibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> - <description>Applies an internal mass recalibration.</description> + <description>Applies an internal mass recalibration</description> <macros> <token name="@EXECUTABLE@">InternalCalibration</token> <import>macros.xml</import> @@ -15,15 +14,15 @@ ## Preprocessing mkdir in && -ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && mkdir out && #if $cal.id_in: mkdir cal.id_in && - ln -s '$cal.id_in' 'cal.id_in/${re.sub("[^\w\-_]", "_", $cal.id_in.element_identifier)}.$gxy2omsext($cal.id_in.ext)' && + cp '$cal.id_in' 'cal.id_in/${re.sub("[^\w\-_]", "_", $cal.id_in.element_identifier)}.$gxy2omsext($cal.id_in.ext)' && #end if #if $cal.lock_in: mkdir cal.lock_in && - ln -s '$cal.lock_in' 'cal.lock_in/${re.sub("[^\w\-_]", "_", $cal.lock_in.element_identifier)}.$gxy2omsext($cal.lock_in.ext)' && + cp '$cal.lock_in' 'cal.lock_in/${re.sub("[^\w\-_]", "_", $cal.lock_in.element_identifier)}.$gxy2omsext($cal.lock_in.ext)' && #end if #if "lock_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') mkdir cal_lock_out && @@ -118,18 +117,18 @@ <configfile name="hardcoded_json"><![CDATA[{"rscript_executable": "Rscript", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> </configfiles> <inputs> - <param argument="-in" type="data" format="mzml" optional="false" label="Input peak file" help=" select mzml data sets(s)"/> - <param argument="-ppm_match_tolerance" type="float" optional="true" value="25.0" label="Finding calibrants in raw data uses this tolerance (for lock masses and ID's)" help=""/> - <param argument="-ms_level" type="text" optional="true" value="1 2 3" label="Target MS levels to apply the transformation onto" help="Does not affect calibrant collection (space separated list, in order to allow for spaces in list items surround them by single quotes)"> + <param argument="-in" type="data" format="mzml" label="Input peak file" help=" select mzml data sets(s)"/> + <param argument="-ppm_match_tolerance" type="float" value="25.0" label="Finding calibrants in raw data uses this tolerance (for lock masses and ID's)" help=""/> + <param argument="-ms_level" type="text" value="1 2 3" label="Target MS levels to apply the transformation onto" help="Does not affect calibrant collection (space separated list, in order to allow for spaces in list items surround them by single quotes)"> <expand macro="list_integer_valsan" name="ms_level"/> </param> - <param argument="-RT_chunking" type="float" optional="true" value="300.0" label="RT window (one-sided" help="i.e. left->center, or center->right) around an MS scan in which calibrants are collected to build a model. Set to -1 to use ALL calibrants for all scans, i.e. a global model"/> + <param argument="-RT_chunking" type="float" value="300.0" label="RT window (one-sided" help="i.e. left->center, or center->right) around an MS scan in which calibrants are collected to build a model. Set to -1 to use ALL calibrants for all scans, i.e. a global model"/> <section name="cal" title="Chose one of two optional input files ('id_in' or 'lock_in') to define the calibration masses/function" help="" expanded="false"> <param name="id_in" argument="-cal:id_in" type="data" format="featurexml,idxml" optional="true" label="Identifications or features whose peptide ID's serve as calibration masses" help=" select featurexml,idxml data sets(s)"/> <param name="lock_in" argument="-cal:lock_in" type="data" format="csv" optional="true" label="Input file containing reference m/z values (text file with each line as: m/z ms-level charge) which occur in all scans" help=" select csv data sets(s)"/> <param name="lock_require_mono" argument="-cal:lock_require_mono" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require all lock masses to be monoisotopic" help="i.e. not the iso1, iso2 etc ('charge' column is used to determine the spacing). Peaks which are not mono-isotopic are not used"/> <param name="lock_require_iso" argument="-cal:lock_require_iso" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Require all lock masses to have at least the +1 isotope" help="Peaks without isotope pattern are not used"/> - <param name="model_type" argument="-cal:model_type" type="select" optional="true" label="Type of function to be fitted to the calibration points" help=""> + <param name="model_type" argument="-cal:model_type" type="select" label="Type of function to be fitted to the calibration points" help=""> <option value="linear">linear</option> <option value="linear_weighted" selected="true">linear_weighted</option> <option value="quadratic">quadratic</option> @@ -139,17 +138,17 @@ </section> <section name="RANSAC" title="Robust outlier removal using RANSAC" help="" expanded="false"> <param name="enabled" argument="-RANSAC:enabled" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply RANSAC to calibration points to remove outliers before fitting a model" help=""/> - <param name="threshold" argument="-RANSAC:threshold" type="float" optional="true" value="10.0" label="Threshold for accepting inliers (instrument precision (not accuracy!) as ppm^2 distance)" help=""/> - <param name="pc_inliers" argument="-RANSAC:pc_inliers" type="integer" optional="true" min="1" max="99" value="30" label="Minimum percentage (of available data) of inliers (<threshold away from model) to accept the model" help=""/> - <param name="iter" argument="-RANSAC:iter" type="integer" optional="true" value="70" label="Maximal # iterations" help=""/> + <param name="threshold" argument="-RANSAC:threshold" type="float" value="10.0" label="Threshold for accepting inliers (instrument precision (not accuracy!) as ppm^2 distance)" help=""/> + <param name="pc_inliers" argument="-RANSAC:pc_inliers" type="integer" min="1" max="99" value="30" label="Minimum percentage (of available data) of inliers (<threshold away from model) to accept the model" help=""/> + <param name="iter" argument="-RANSAC:iter" type="integer" value="70" label="Maximal # iterations" help=""/> </section> <section name="goodness" title="Thresholds for accepting calibration success" help="" expanded="false"> - <param name="median" argument="-goodness:median" type="float" optional="true" value="4.0" label="The median ppm error of calibrated masses must be smaller than this threshold" help=""/> - <param name="MAD" argument="-goodness:MAD" type="float" optional="true" value="2.0" label="The median absolute deviation of the ppm error of calibrated masses must be smaller than this threshold" help=""/> + <param name="median" argument="-goodness:median" type="float" value="4.0" label="The median ppm error of calibrated masses must be smaller than this threshold" help=""/> + <param name="MAD" argument="-goodness:MAD" type="float" value="2.0" label="The median absolute deviation of the ppm error of calibrated masses must be smaller than this threshold" help=""/> </section> <expand macro="adv_opts_macro"> <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> - <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> <expand macro="list_string_san" name="test"/> </param> </expand> @@ -187,14 +186,15 @@ <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> </data> </outputs> - <tests><!-- TOPP_InternalCalibration_1 --> + <tests> + <!-- TOPP_InternalCalibration_1 --> <test expect_num_outputs="4"> <section name="adv_opts"> <param name="force" value="false"/> <param name="test" value="true"/> </section> <param name="in" value="InternalCalibration_1_BSA1.mzML"/> - <output name="out" file="InternalCalibration_1_BSA1_out.mzML.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <output name="out" value="InternalCalibration_1_BSA1_out.mzML.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <param name="ppm_match_tolerance" value="25.0"/> <param name="ms_level" value="1"/> <param name="RT_chunking" value="-1.0"/> @@ -215,14 +215,17 @@ <param name="MAD" value="2.0"/> </section> <section name="quality_control"/> - <output name="quality_control_models" file="InternalCalibration_1_models.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/> - <output name="quality_control_residuals" file="InternalCalibration_1_residuals.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="quality_control_models" value="InternalCalibration_1_models.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="quality_control_residuals" value="InternalCalibration_1_residuals.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> <!-- TOPP_InternalCalibration_2 --> <test expect_num_outputs="4"> @@ -231,7 +234,7 @@ <param name="test" value="true"/> </section> <param name="in" value="InternalCalibration_2_lockmass.mzML.gz"/> - <output name="out" file="InternalCalibration_2_lockmass.mzML.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/> + <output name="out" value="InternalCalibration_2_lockmass.mzML.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/> <param name="ppm_match_tolerance" value="25.0"/> <param name="ms_level" value="1 2 3"/> <param name="RT_chunking" value="60.0"/> @@ -252,19 +255,22 @@ <param name="MAD" value="2.0"/> </section> <section name="quality_control"/> - <output name="quality_control_models" file="InternalCalibration_2_models.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/> - <output name="quality_control_residuals" file="InternalCalibration_2_residuals.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="quality_control_models" value="InternalCalibration_2_models.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/> + <output name="quality_control_residuals" value="InternalCalibration_2_residuals.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/> <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/> <output name="ctd_out" ftype="xml"> <assert_contents> <is_valid_xml/> </assert_contents> </output> + <assert_stdout> + <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/> + </assert_stdout> </test> </tests> <help><![CDATA[Applies an internal mass recalibration. -For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_InternalCalibration.html]]></help> +For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_InternalCalibration.html]]></help> <expand macro="references"/> </tool>