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comparison InternalCalibration.xml @ 13:f49a58e03ada draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:14:27 +0000
parents 6c58aa0ed5c1
children a1dffbb8fbc3
comparison
equal deleted inserted replaced
12:f75fb96bb742 13:f49a58e03ada
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Signal processing and preprocessing]--> 3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
4 <tool id="InternalCalibration" name="InternalCalibration" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="InternalCalibration" name="InternalCalibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Applies an internal mass recalibration.</description> 5 <description>Applies an internal mass recalibration.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">InternalCalibration</token> 7 <token name="@EXECUTABLE@">InternalCalibration</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
118 <configfiles> 116 <configfiles>
119 <inputs name="args_json" data_style="paths"/> 117 <inputs name="args_json" data_style="paths"/>
120 <configfile name="hardcoded_json"><![CDATA[{"rscript_executable": "Rscript", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 118 <configfile name="hardcoded_json"><![CDATA[{"rscript_executable": "Rscript", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
121 </configfiles> 119 </configfiles>
122 <inputs> 120 <inputs>
123 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input peak file" help=" select mzml data sets(s)"/> 121 <param argument="-in" type="data" format="mzml" optional="false" label="Input peak file" help=" select mzml data sets(s)"/>
124 <param name="ppm_match_tolerance" 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=""/> 122 <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=""/>
125 <param name="ms_level" 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)"> 123 <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)">
126 <expand macro="list_integer_valsan"/> 124 <expand macro="list_integer_valsan" name="ms_level"/>
127 </param> 125 </param>
128 <param name="RT_chunking" argument="-RT_chunking" type="float" optional="true" value="300.0" label="RT window (one-sided" help="i.e. left-&gt;center, or center-&gt;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"/> 126 <param argument="-RT_chunking" type="float" optional="true" value="300.0" label="RT window (one-sided" help="i.e. left-&gt;center, or center-&gt;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"/>
129 <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"> 127 <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">
130 <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)"/> 128 <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)"/>
131 <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)"/> 129 <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)"/>
132 <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"/> 130 <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"/>
133 <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"/> 131 <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"/>
134 <param name="model_type" argument="-cal:model_type" display="radio" type="select" optional="false" label="Type of function to be fitted to the calibration points" help=""> 132 <param name="model_type" argument="-cal:model_type" type="select" optional="true" label="Type of function to be fitted to the calibration points" help="">
135 <option value="linear">linear</option> 133 <option value="linear">linear</option>
136 <option value="linear_weighted" selected="true">linear_weighted</option> 134 <option value="linear_weighted" selected="true">linear_weighted</option>
137 <option value="quadratic">quadratic</option> 135 <option value="quadratic">quadratic</option>
138 <option value="quadratic_weighted">quadratic_weighted</option> 136 <option value="quadratic_weighted">quadratic_weighted</option>
139 <expand macro="list_string_san"/> 137 <expand macro="list_string_san" name="model_type"/>
140 </param> 138 </param>
141 </section> 139 </section>
142 <section name="RANSAC" title="Robust outlier removal using RANSAC" help="" expanded="false"> 140 <section name="RANSAC" title="Robust outlier removal using RANSAC" help="" expanded="false">
143 <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=""/> 141 <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=""/>
144 <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=""/> 142 <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=""/>
148 <section name="goodness" title="Thresholds for accepting calibration success" help="" expanded="false"> 146 <section name="goodness" title="Thresholds for accepting calibration success" help="" expanded="false">
149 <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=""/> 147 <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=""/>
150 <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=""/> 148 <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=""/>
151 </section> 149 </section>
152 <expand macro="adv_opts_macro"> 150 <expand macro="adv_opts_macro">
153 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 151 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
154 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 152 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
155 <expand macro="list_string_san"/> 153 <expand macro="list_string_san" name="test"/>
156 </param> 154 </param>
157 </expand> 155 </expand>
158 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 156 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
159 <option value="lock_out_FLAG">lock_out (Optional output file containing peaks from 'in' which were matched to reference m/z values)</option> 157 <option value="lock_out_FLAG">lock_out (Optional output file containing peaks from 'in' which were matched to reference m/z values)</option>
160 <option value="lock_fail_out_FLAG">lock_fail_out (Optional output file containing lock masses which were NOT found or accepted(!) in data from 'in')</option> 158 <option value="lock_fail_out_FLAG">lock_fail_out (Optional output file containing lock masses which were NOT found or accepted(!) in data from 'in')</option>
187 </data> 185 </data>
188 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 186 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
189 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 187 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
190 </data> 188 </data>
191 </outputs> 189 </outputs>
192 <tests> 190 <tests><!-- TOPP_InternalCalibration_1 -->
193 <expand macro="autotest_InternalCalibration"/> 191 <test expect_num_outputs="4">
194 <expand macro="manutest_InternalCalibration"/> 192 <section name="adv_opts">
193 <param name="force" value="false"/>
194 <param name="test" value="true"/>
195 </section>
196 <param name="in" value="InternalCalibration_1_BSA1.mzML"/>
197 <output name="out" file="InternalCalibration_1_BSA1_out.mzML.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
198 <param name="ppm_match_tolerance" value="25.0"/>
199 <param name="ms_level" value="1"/>
200 <param name="RT_chunking" value="-1.0"/>
201 <section name="cal">
202 <param name="id_in" value="InternalCalibration_1_BSA1_OMSSA.idXML"/>
203 <param name="lock_require_mono" value="false"/>
204 <param name="lock_require_iso" value="false"/>
205 <param name="model_type" value="linear"/>
206 </section>
207 <section name="RANSAC">
208 <param name="enabled" value="true"/>
209 <param name="threshold" value="1.0"/>
210 <param name="pc_inliers" value="30"/>
211 <param name="iter" value="500"/>
212 </section>
213 <section name="goodness">
214 <param name="median" value="4.0"/>
215 <param name="MAD" value="2.0"/>
216 </section>
217 <section name="quality_control"/>
218 <output name="quality_control_models" file="InternalCalibration_1_models.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
219 <output name="quality_control_residuals" file="InternalCalibration_1_residuals.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
220 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/>
221 <output name="ctd_out" ftype="xml">
222 <assert_contents>
223 <is_valid_xml/>
224 </assert_contents>
225 </output>
226 </test>
227 <!-- TOPP_InternalCalibration_2 -->
228 <test expect_num_outputs="4">
229 <section name="adv_opts">
230 <param name="force" value="false"/>
231 <param name="test" value="true"/>
232 </section>
233 <param name="in" value="InternalCalibration_2_lockmass.mzML.gz"/>
234 <output name="out" file="InternalCalibration_2_lockmass.mzML.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
235 <param name="ppm_match_tolerance" value="25.0"/>
236 <param name="ms_level" value="1 2 3"/>
237 <param name="RT_chunking" value="60.0"/>
238 <section name="cal">
239 <param name="lock_in" value="InternalCalibration_2_lock.csv" ftype="csv"/>
240 <param name="lock_require_mono" value="true"/>
241 <param name="lock_require_iso" value="false"/>
242 <param name="model_type" value="linear"/>
243 </section>
244 <section name="RANSAC">
245 <param name="enabled" value="false"/>
246 <param name="threshold" value="10.0"/>
247 <param name="pc_inliers" value="30"/>
248 <param name="iter" value="70"/>
249 </section>
250 <section name="goodness">
251 <param name="median" value="4.0"/>
252 <param name="MAD" value="2.0"/>
253 </section>
254 <section name="quality_control"/>
255 <output name="quality_control_models" file="InternalCalibration_2_models.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
256 <output name="quality_control_residuals" file="InternalCalibration_2_residuals.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/>
257 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/>
258 <output name="ctd_out" ftype="xml">
259 <assert_contents>
260 <is_valid_xml/>
261 </assert_contents>
262 </output>
263 </test>
195 </tests> 264 </tests>
196 <help><![CDATA[Applies an internal mass recalibration. 265 <help><![CDATA[Applies an internal mass recalibration.
197 266
198 267
199 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_InternalCalibration.html]]></help> 268 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_InternalCalibration.html]]></help>
200 <expand macro="references"/> 269 <expand macro="references"/>
201 </tool> 270 </tool>