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comparison InternalCalibration.xml @ 14:a1dffbb8fbc3 draft default tip

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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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13:f49a58e03ada 14:a1dffbb8fbc3
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.--> 1 <!--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]--> 2 <!--Proposed Tool Section: [Mass Correction and Calibration]-->
4 <tool id="InternalCalibration" name="InternalCalibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="InternalCalibration" name="InternalCalibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Applies an internal mass recalibration.</description> 4 <description>Applies an internal mass recalibration</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">InternalCalibration</token> 6 <token name="@EXECUTABLE@">InternalCalibration</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir out && 18 mkdir out &&
20 #if $cal.id_in: 19 #if $cal.id_in:
21 mkdir cal.id_in && 20 mkdir cal.id_in &&
22 ln -s '$cal.id_in' 'cal.id_in/${re.sub("[^\w\-_]", "_", $cal.id_in.element_identifier)}.$gxy2omsext($cal.id_in.ext)' && 21 cp '$cal.id_in' 'cal.id_in/${re.sub("[^\w\-_]", "_", $cal.id_in.element_identifier)}.$gxy2omsext($cal.id_in.ext)' &&
23 #end if 22 #end if
24 #if $cal.lock_in: 23 #if $cal.lock_in:
25 mkdir cal.lock_in && 24 mkdir cal.lock_in &&
26 ln -s '$cal.lock_in' 'cal.lock_in/${re.sub("[^\w\-_]", "_", $cal.lock_in.element_identifier)}.$gxy2omsext($cal.lock_in.ext)' && 25 cp '$cal.lock_in' 'cal.lock_in/${re.sub("[^\w\-_]", "_", $cal.lock_in.element_identifier)}.$gxy2omsext($cal.lock_in.ext)' &&
27 #end if 26 #end if
28 #if "lock_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 27 #if "lock_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
29 mkdir cal_lock_out && 28 mkdir cal_lock_out &&
30 #end if 29 #end if
31 #if "lock_fail_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 30 #if "lock_fail_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
116 <configfiles> 115 <configfiles>
117 <inputs name="args_json" data_style="paths"/> 116 <inputs name="args_json" data_style="paths"/>
118 <configfile name="hardcoded_json"><![CDATA[{"rscript_executable": "Rscript", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 117 <configfile name="hardcoded_json"><![CDATA[{"rscript_executable": "Rscript", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
119 </configfiles> 118 </configfiles>
120 <inputs> 119 <inputs>
121 <param argument="-in" type="data" format="mzml" optional="false" label="Input peak file" help=" select mzml data sets(s)"/> 120 <param argument="-in" type="data" format="mzml" label="Input peak file" help=" select mzml data sets(s)"/>
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=""/> 121 <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=""/>
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)"> 122 <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)">
124 <expand macro="list_integer_valsan" name="ms_level"/> 123 <expand macro="list_integer_valsan" name="ms_level"/>
125 </param> 124 </param>
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"/> 125 <param argument="-RT_chunking" type="float" 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"/>
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"> 126 <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">
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)"/> 127 <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)"/>
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)"/> 128 <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)"/>
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"/> 129 <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"/>
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"/> 130 <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"/>
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=""> 131 <param name="model_type" argument="-cal:model_type" type="select" label="Type of function to be fitted to the calibration points" help="">
133 <option value="linear">linear</option> 132 <option value="linear">linear</option>
134 <option value="linear_weighted" selected="true">linear_weighted</option> 133 <option value="linear_weighted" selected="true">linear_weighted</option>
135 <option value="quadratic">quadratic</option> 134 <option value="quadratic">quadratic</option>
136 <option value="quadratic_weighted">quadratic_weighted</option> 135 <option value="quadratic_weighted">quadratic_weighted</option>
137 <expand macro="list_string_san" name="model_type"/> 136 <expand macro="list_string_san" name="model_type"/>
138 </param> 137 </param>
139 </section> 138 </section>
140 <section name="RANSAC" title="Robust outlier removal using RANSAC" help="" expanded="false"> 139 <section name="RANSAC" title="Robust outlier removal using RANSAC" help="" expanded="false">
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=""/> 140 <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=""/>
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=""/> 141 <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=""/>
143 <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 (&lt;threshold away from model) to accept the model" help=""/> 142 <param name="pc_inliers" argument="-RANSAC:pc_inliers" type="integer" min="1" max="99" value="30" label="Minimum percentage (of available data) of inliers (&lt;threshold away from model) to accept the model" help=""/>
144 <param name="iter" argument="-RANSAC:iter" type="integer" optional="true" value="70" label="Maximal # iterations" help=""/> 143 <param name="iter" argument="-RANSAC:iter" type="integer" value="70" label="Maximal # iterations" help=""/>
145 </section> 144 </section>
146 <section name="goodness" title="Thresholds for accepting calibration success" help="" expanded="false"> 145 <section name="goodness" title="Thresholds for accepting calibration success" help="" expanded="false">
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=""/> 146 <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=""/>
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=""/> 147 <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=""/>
149 </section> 148 </section>
150 <expand macro="adv_opts_macro"> 149 <expand macro="adv_opts_macro">
151 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 150 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
152 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 151 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
153 <expand macro="list_string_san" name="test"/> 152 <expand macro="list_string_san" name="test"/>
154 </param> 153 </param>
155 </expand> 154 </expand>
156 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 155 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
157 <option value="lock_out_FLAG">lock_out (Optional output file containing peaks from 'in' which were matched to reference m/z values)</option> 156 <option value="lock_out_FLAG">lock_out (Optional output file containing peaks from 'in' which were matched to reference m/z values)</option>
185 </data> 184 </data>
186 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 185 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
187 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 186 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
188 </data> 187 </data>
189 </outputs> 188 </outputs>
190 <tests><!-- TOPP_InternalCalibration_1 --> 189 <tests>
190 <!-- TOPP_InternalCalibration_1 -->
191 <test expect_num_outputs="4"> 191 <test expect_num_outputs="4">
192 <section name="adv_opts"> 192 <section name="adv_opts">
193 <param name="force" value="false"/> 193 <param name="force" value="false"/>
194 <param name="test" value="true"/> 194 <param name="test" value="true"/>
195 </section> 195 </section>
196 <param name="in" value="InternalCalibration_1_BSA1.mzML"/> 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"/> 197 <output name="out" value="InternalCalibration_1_BSA1_out.mzML.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
198 <param name="ppm_match_tolerance" value="25.0"/> 198 <param name="ppm_match_tolerance" value="25.0"/>
199 <param name="ms_level" value="1"/> 199 <param name="ms_level" value="1"/>
200 <param name="RT_chunking" value="-1.0"/> 200 <param name="RT_chunking" value="-1.0"/>
201 <section name="cal"> 201 <section name="cal">
202 <param name="id_in" value="InternalCalibration_1_BSA1_OMSSA.idXML"/> 202 <param name="id_in" value="InternalCalibration_1_BSA1_OMSSA.idXML"/>
213 <section name="goodness"> 213 <section name="goodness">
214 <param name="median" value="4.0"/> 214 <param name="median" value="4.0"/>
215 <param name="MAD" value="2.0"/> 215 <param name="MAD" value="2.0"/>
216 </section> 216 </section>
217 <section name="quality_control"/> 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"/> 218 <output name="quality_control_models" value="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"/> 219 <output name="quality_control_residuals" value="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"/> 220 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/>
221 <output name="ctd_out" ftype="xml"> 221 <output name="ctd_out" ftype="xml">
222 <assert_contents> 222 <assert_contents>
223 <is_valid_xml/> 223 <is_valid_xml/>
224 </assert_contents> 224 </assert_contents>
225 </output> 225 </output>
226 <assert_stdout>
227 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
228 </assert_stdout>
226 </test> 229 </test>
227 <!-- TOPP_InternalCalibration_2 --> 230 <!-- TOPP_InternalCalibration_2 -->
228 <test expect_num_outputs="4"> 231 <test expect_num_outputs="4">
229 <section name="adv_opts"> 232 <section name="adv_opts">
230 <param name="force" value="false"/> 233 <param name="force" value="false"/>
231 <param name="test" value="true"/> 234 <param name="test" value="true"/>
232 </section> 235 </section>
233 <param name="in" value="InternalCalibration_2_lockmass.mzML.gz"/> 236 <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"/> 237 <output name="out" value="InternalCalibration_2_lockmass.mzML.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
235 <param name="ppm_match_tolerance" value="25.0"/> 238 <param name="ppm_match_tolerance" value="25.0"/>
236 <param name="ms_level" value="1 2 3"/> 239 <param name="ms_level" value="1 2 3"/>
237 <param name="RT_chunking" value="60.0"/> 240 <param name="RT_chunking" value="60.0"/>
238 <section name="cal"> 241 <section name="cal">
239 <param name="lock_in" value="InternalCalibration_2_lock.csv" ftype="csv"/> 242 <param name="lock_in" value="InternalCalibration_2_lock.csv" ftype="csv"/>
250 <section name="goodness"> 253 <section name="goodness">
251 <param name="median" value="4.0"/> 254 <param name="median" value="4.0"/>
252 <param name="MAD" value="2.0"/> 255 <param name="MAD" value="2.0"/>
253 </section> 256 </section>
254 <section name="quality_control"/> 257 <section name="quality_control"/>
255 <output name="quality_control_models" file="InternalCalibration_2_models.csv" compare="sim_size" delta_frac="0.7" ftype="csv"/> 258 <output name="quality_control_models" value="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"/> 259 <output name="quality_control_residuals" value="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"/> 260 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,models_FLAG,residuals_FLAG"/>
258 <output name="ctd_out" ftype="xml"> 261 <output name="ctd_out" ftype="xml">
259 <assert_contents> 262 <assert_contents>
260 <is_valid_xml/> 263 <is_valid_xml/>
261 </assert_contents> 264 </assert_contents>
262 </output> 265 </output>
266 <assert_stdout>
267 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
268 </assert_stdout>
263 </test> 269 </test>
264 </tests> 270 </tests>
265 <help><![CDATA[Applies an internal mass recalibration. 271 <help><![CDATA[Applies an internal mass recalibration.
266 272
267 273
268 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_InternalCalibration.html]]></help> 274 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_InternalCalibration.html]]></help>
269 <expand macro="references"/> 275 <expand macro="references"/>
270 </tool> 276 </tool>